[Binari] [Fwd: Re:Re: Fw: A PHD student using splice machine]
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-( ---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> -------------------------------------------------------------------------- Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why? Best regards! Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
------------------------------------------------------------------------ *From*: ¿µÑ©æ¯ <kxj19840724@126.com> *To*: yves.vandepeer@psb.vib-ugent.be <yves.vandepeer@psb.vib-ugent.be> *Sent*: Fri Jun 25 08:31:52 2010 *Subject*: A PHD student using splice machine
Dear Professor I'm a PHD student doing research in splice sites prediction and I have read your article"Splice Machine: predicting splice sites from high-dimensional local context representations". Now I want to do some comparisons on NN269 acceptor datasets, but I don't know how to use the software(how to do prediction). Would you like to tell me the details? Best wishes to you and your family! Thanks a lot!
Yours sincerely Kang xuejiao
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
-- Michiel Van Bel PhD student VIB, UGent Technologiepark 927, B-9052 GENT
looks like the average help request mail overhere :) Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
------------------------------------------------------------------------ *From*: ¿µÑ©æ¯ <kxj19840724@126.com> *To*: yves.vandepeer@psb.vib-ugent.be <yves.vandepeer@psb.vib-ugent.be> *Sent*: Fri Jun 25 08:31:52 2010 *Subject*: A PHD student using splice machine
Dear Professor I'm a PHD student doing research in splice sites prediction and I have read your article"Splice Machine: predicting splice sites from high-dimensional local context representations". Now I want to do some comparisons on NN269 acceptor datasets, but I don't know how to use the software(how to do prediction). Would you like to tell me the details? Best wishes to you and your family! Thanks a lot!
Yours sincerely Kang xuejiao
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be
http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
------------------------------------------------------------------------ *From*: ¿µÑ©æ¯ <kxj19840724@126.com> *To*: yves.vandepeer@psb.vib-ugent.be <yves.vandepeer@psb.vib-ugent.be> *Sent*: Fri Jun 25 08:31:52 2010 *Subject*: A PHD student using splice machine
Dear Professor I'm a PHD student doing research in splice sites prediction and I have read your article"Splice Machine: predicting splice sites from high-dimensional local context representations". Now I want to do some comparisons on NN269 acceptor datasets, but I don't know how to use the software(how to do prediction). Would you like to tell me the details? Best wishes to you and your family! Thanks a lot!
Yours sincerely Kang xuejiao
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
and don't you just love their very descriptive email address .. ;) On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
------------------------------------------------------------------------ *From*: ¿µÑ©æ¯ <kxj19840724@126.com> *To*: yves.vandepeer@psb.vib-ugent.be <yves.vandepeer@psb.vib-ugent.be> *Sent*: Fri Jun 25 08:31:52 2010 *Subject*: A PHD student using splice machine
Dear Professor I'm a PHD student doing research in splice sites prediction and I have read your article"Splice Machine: predicting splice sites from high-dimensional local context representations". Now I want to do some comparisons on NN269 acceptor datasets, but I don't know how to use the software(how to do prediction). Would you like to tell me the details? Best wishes to you and your family! Thanks a lot!
Yours sincerely Kang xuejiao
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be
http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
------------------------------------------------------------------------ *From*: ¿µÑ©æ¯ <kxj19840724@126.com> *To*: yves.vandepeer@psb.vib-ugent.be <yves.vandepeer@psb.vib-ugent.be> *Sent*: Fri Jun 25 08:31:52 2010 *Subject*: A PHD student using splice machine
Dear Professor I'm a PHD student doing research in splice sites prediction and I have read your article"Splice Machine: predicting splice sites from high-dimensional local context representations". Now I want to do some comparisons on NN269 acceptor datasets, but I don't know how to use the software(how to do prediction). Would you like to tell me the details? Best wishes to you and your family! Thanks a lot!
Yours sincerely Kang xuejiao
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ======================================================================
born the 24th of july 1984 ? Kenny Billiau wrote:
and don't you just love their very descriptive email address .. ;)
On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote:
> ------------------------------------------------------------------------ > > *From*: ¿µÑ©æ¯ <kxj19840724@126.com> > *To*: yves.vandepeer@psb.vib-ugent.be > <yves.vandepeer@psb.vib-ugent.be> > *Sent*: Fri Jun 25 08:31:52 2010 > *Subject*: A PHD student using splice machine > > Dear Professor > I'm a PHD student doing research in splice sites prediction > and I have read your article"Splice Machine: predicting splice > sites > from high-dimensional local context representations". Now I want > to do > some comparisons on NN269 acceptor datasets, but I don't know > how to > use the software(how to do prediction). Would you like to tell > me the > details? > Best wishes to you and your family! > Thanks a lot! > > > Yours sincerely > Kang xuejiao > > > -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be
http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
Hi Kang, you can run the splicemachine software at this location: http://bioinformatics.psb.ugent.be/webtools/splicemachine/
Just copy-paste the sequences in fasta format into the text-field, and press the "run splicemachine" button.
kind regards, Michiel
Yves Van De Peer wrote: > > ------------------------------------------------------------------------ > > *From*: ¿µÑ©æ¯ <kxj19840724@126.com> > *To*: yves.vandepeer@psb.vib-ugent.be > <yves.vandepeer@psb.vib-ugent.be> > *Sent*: Fri Jun 25 08:31:52 2010 > *Subject*: A PHD student using splice machine > > Dear Professor > I'm a PHD student doing research in splice sites prediction > and I have read your article"Splice Machine: predicting splice > sites > from high-dimensional local context representations". Now I want > to do > some comparisons on NN269 acceptor datasets, but I don't know > how to > use the software(how to do prediction). Would you like to tell > me the > details? > Best wishes to you and your family! > Thanks a lot! > > > Yours sincerely > Kang xuejiao > >
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ====================================================================== ------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
I bet he gets loads of presents this way .. On Mon, 28 Jun 2010, Frederik Delaere wrote:
born the 24th of july 1984 ?
Kenny Billiau wrote:
and don't you just love their very descriptive email address .. ;)
On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
> Hi Kang, > you can run the splicemachine software at this location: > http://bioinformatics.psb.ugent.be/webtools/splicemachine/ > > Just copy-paste the sequences in fasta format into the > text-field, and > press the "run splicemachine" button. > > kind regards, > Michiel > > > > Yves Van De Peer wrote: > >> ------------------------------------------------------------------------ >> >> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >> *To*: yves.vandepeer@psb.vib-ugent.be >> <yves.vandepeer@psb.vib-ugent.be> >> *Sent*: Fri Jun 25 08:31:52 2010 >> *Subject*: A PHD student using splice machine >> >> Dear Professor >> I'm a PHD student doing research in splice sites prediction >> and I have read your article"Splice Machine: predicting splice >> sites >> from high-dimensional local context representations". Now I want >> to do >> some comparisons on NN269 acceptor datasets, but I don't know >> how to >> use the software(how to do prediction). Would you like to tell >> me the >> details? >> Best wishes to you and your family! >> Thanks a lot! >> >> >> Yours sincerely >> Kang xuejiao >> >> >> > -- > ================================================================== > Michiel Van Bel > PhD student > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > mibel@psb.vib-ugent.be > http://www.psb.vib-ugent.be
> http://bioinformatics.psb.ugent.be > ================================================================== > > >
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
Hi Michieal Thanks for your reply! Here I want to know how to run the software.To the inputing file, how to distinguish the training file and the testing file?or the all the data should be in one file?Then how to distinguish the true or false sites? Thanks a lot! Regards! Xuejiao
> Hi Kang, > you can run the splicemachine software at this location: > http://bioinformatics.psb.ugent.be/webtools/splicemachine/ > > Just copy-paste the sequences in fasta format into the > text-field, and > press the "run splicemachine" button. > > kind regards, > Michiel > > > > Yves Van De Peer wrote: >> >> ------------------------------------------------------------------------ >> >> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >> *To*: yves.vandepeer@psb.vib-ugent.be >> <yves.vandepeer@psb.vib-ugent.be> >> *Sent*: Fri Jun 25 08:31:52 2010 >> *Subject*: A PHD student using splice machine >> >> Dear Professor >> I'm a PHD student doing research in splice sites prediction >> and I have read your article"Splice Machine: predicting splice >> sites >> from high-dimensional local context representations". Now I want >> to do >> some comparisons on NN269 acceptor datasets, but I don't know >> how to >> use the software(how to do prediction). Would you like to tell >> me the >> details? >> Best wishes to you and your family! >> Thanks a lot! >> >> >> Yours sincerely >> Kang xuejiao >> >> > > > -- > ================================================================== > Michiel Van Bel > PhD student > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > mibel@psb.vib-ugent.be > http://www.psb.vib-ugent.be > http://bioinformatics.psb.ugent.be > ================================================================== > >
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ====================================================================== ------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere
Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ======================================================================
presents, you say? On 06/28/2010 12:58 PM, Kenny Billiau wrote:
I bet he gets loads of presents this way ..
On Mon, 28 Jun 2010, Frederik Delaere wrote:
born the 24th of july 1984 ?
Kenny Billiau wrote:
and don't you just love their very descriptive email address .. ;)
On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote:
> Hi Michieal > Thanks for your reply! > Here I want to know how to run the software.To the inputing > file, how > to distinguish the training file and the testing file?or the all > the > data should be in one file?Then how to distinguish the true or > false > sites? > Thanks a lot! > Regards! > Xuejiao > > > >> Hi Kang, >> you can run the splicemachine software at this location: >> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >> >> Just copy-paste the sequences in fasta format into the >> text-field, and >> press the "run splicemachine" button. >> >> kind regards, >> Michiel >> >> >> >> Yves Van De Peer wrote: >> >>> ------------------------------------------------------------------------ >>> >>> >>> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >>> *To*: yves.vandepeer@psb.vib-ugent.be >>> <yves.vandepeer@psb.vib-ugent.be> >>> *Sent*: Fri Jun 25 08:31:52 2010 >>> *Subject*: A PHD student using splice machine >>> >>> Dear Professor >>> I'm a PHD student doing research in splice sites >>> prediction >>> and I have read your article"Splice Machine: predicting splice >>> sites >>> from high-dimensional local context representations". Now I want >>> to do >>> some comparisons on NN269 acceptor datasets, but I don't know >>> how to >>> use the software(how to do prediction). Would you like to tell >>> me the >>> details? >>> Best wishes to you and your family! >>> Thanks a lot! >>> >>> >>> Yours sincerely >>> Kang xuejiao >>> >>> >>> >> -- >> ================================================================== >> Michiel Van Bel >> PhD student >> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> mibel@psb.vib-ugent.be >> http://www.psb.vib-ugent.be
>> http://bioinformatics.psb.ugent.be >> ================================================================== >> >> >> > > -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
ok, the software available on the website is only trained for Arabidopsis and Human. So you can only use a test-file (in fasta format). The output-format is described here: http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/
In order to train splicemachine yourself, you'll have to use the offline installation (see attachment). However, as I didn't write the software, I do not think I can really help you any further with any questions considering training splicemachine yourself. Please have a look at the pdf-files included in the attachment, for any further instructions.
Michiel
¿µÑ©æ¯ wrote: > Hi Michieal > Thanks for your reply! > Here I want to know how to run the software.To the inputing > file, how > to distinguish the training file and the testing file?or the all > the > data should be in one file?Then how to distinguish the true or > false > sites? > Thanks a lot! > Regards! > Xuejiao > > >> Hi Kang, >> you can run the splicemachine software at this location: >> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >> >> Just copy-paste the sequences in fasta format into the >> text-field, and >> press the "run splicemachine" button. >> >> kind regards, >> Michiel >> >> >> >> Yves Van De Peer wrote: >>> >>> ------------------------------------------------------------------------ >>> >>> >>> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >>> *To*: yves.vandepeer@psb.vib-ugent.be >>> <yves.vandepeer@psb.vib-ugent.be> >>> *Sent*: Fri Jun 25 08:31:52 2010 >>> *Subject*: A PHD student using splice machine >>> >>> Dear Professor >>> I'm a PHD student doing research in splice sites >>> prediction >>> and I have read your article"Splice Machine: predicting splice >>> sites >>> from high-dimensional local context representations". Now I want >>> to do >>> some comparisons on NN269 acceptor datasets, but I don't know >>> how to >>> use the software(how to do prediction). Would you like to tell >>> me the >>> details? >>> Best wishes to you and your family! >>> Thanks a lot! >>> >>> >>> Yours sincerely >>> Kang xuejiao >>> >>> >> >> >> -- >> ================================================================== >> Michiel Van Bel >> PhD student >> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> mibel@psb.vib-ugent.be >> http://www.psb.vib-ugent.be >> http://bioinformatics.psb.ugent.be >> ================================================================== >> >> > > >
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ====================================================================== ------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere
Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ======================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
I mailed you a map of a hidden treasure marijn wrote:
presents, you say?
On 06/28/2010 12:58 PM, Kenny Billiau wrote:
I bet he gets loads of presents this way ..
On Mon, 28 Jun 2010, Frederik Delaere wrote:
born the 24th of july 1984 ?
Kenny Billiau wrote:
and don't you just love their very descriptive email address .. ;)
On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
*sigh* sometimes I really want to tell those guys to a) follow a decent english course b) read the fucking manual
I mean, it's not that difficult to read your email again before you send it, and make sure it makes sense :-(
---------------------------- Original Message ---------------------------- Subject: Re:Re: Fw: A PHD student using splice machine From: ¿µÑ©æ¯ <kxj19840724@126.com> Date: Sun, June 27, 2010 4:14 am To: "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be> --------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
> ok, > the software available on the website is only trained for > Arabidopsis > and Human. > So you can only use a test-file (in fasta format). The > output-format is > described here: > http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/ > > In order to train splicemachine yourself, you'll have to use the > offline > installation (see attachment). > However, as I didn't write the software, I do not think I can > really > help you any further with any questions considering training > splicemachine yourself. Please have a look at the pdf-files > included in > the attachment, for any further instructions. > > Michiel > > > > > ¿µÑ©æ¯ wrote: > >> Hi Michieal >> Thanks for your reply! >> Here I want to know how to run the software.To the inputing >> file, how >> to distinguish the training file and the testing file?or the >> all the >> data should be in one file?Then how to distinguish the true or >> false >> sites? >> Thanks a lot! >> Regards! >> Xuejiao >> >> >> >>> Hi Kang, >>> you can run the splicemachine software at this location: >>> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >>> >>> Just copy-paste the sequences in fasta format into the >>> text-field, and >>> press the "run splicemachine" button. >>> >>> kind regards, >>> Michiel >>> >>> >>> >>> Yves Van De Peer wrote: >>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >>>> *To*: yves.vandepeer@psb.vib-ugent.be >>>> <yves.vandepeer@psb.vib-ugent.be> >>>> *Sent*: Fri Jun 25 08:31:52 2010 >>>> *Subject*: A PHD student using splice machine >>>> >>>> Dear Professor >>>> I'm a PHD student doing research in splice sites >>>> prediction >>>> and I have read your article"Splice Machine: predicting splice >>>> sites >>>> from high-dimensional local context representations". Now I want >>>> to do >>>> some comparisons on NN269 acceptor datasets, but I don't know >>>> how to >>>> use the software(how to do prediction). Would you like to tell >>>> me the >>>> details? >>>> Best wishes to you and your family! >>>> Thanks a lot! >>>> >>>> >>>> Yours sincerely >>>> Kang xuejiao >>>> >>>> >>>> >>> -- >>> ================================================================== >>> >>> Michiel Van Bel >>> PhD student >>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>> 3313809 >>> VIB Department of Plant Systems Biology, Ghent University >>> Technologiepark 927, 9052 Gent, BELGIUM >>> mibel@psb.vib-ugent.be >>> http://www.psb.vib-ugent.be
>>> http://bioinformatics.psb.ugent.be >>> ================================================================== >>> >>> >>> >>> >> >> > -- > ================================================================== > Michiel Van Bel > PhD student > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > mibel@psb.vib-ugent.be > http://www.psb.vib-ugent.be > http://bioinformatics.psb.ugent.be > ================================================================== > > >
------------------------------------------------------------------------
Dear Michiel Thanks for your help! I have tried to predict my test file using the software but the annotation file can be downloaded,why?
Best regards!
Xuejiao
> ok, > the software available on the website is only trained for > Arabidopsis > and Human. > So you can only use a test-file (in fasta format). The > output-format is > described here: > http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/ > > In order to train splicemachine yourself, you'll have to use the > offline > installation (see attachment). > However, as I didn't write the software, I do not think I can > really > help you any further with any questions considering training > splicemachine yourself. Please have a look at the pdf-files > included in > the attachment, for any further instructions. > > Michiel > > > > > ¿µÑ©æ¯ wrote: >> Hi Michieal >> Thanks for your reply! >> Here I want to know how to run the software.To the inputing >> file, how >> to distinguish the training file and the testing file?or the >> all the >> data should be in one file?Then how to distinguish the true or >> false >> sites? >> Thanks a lot! >> Regards! >> Xuejiao >> >> >>> Hi Kang, >>> you can run the splicemachine software at this location: >>> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >>> >>> Just copy-paste the sequences in fasta format into the >>> text-field, and >>> press the "run splicemachine" button. >>> >>> kind regards, >>> Michiel >>> >>> >>> >>> Yves Van De Peer wrote: >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> *From*: ¿µÑ©æ¯ <kxj19840724@126.com> >>>> *To*: yves.vandepeer@psb.vib-ugent.be >>>> <yves.vandepeer@psb.vib-ugent.be> >>>> *Sent*: Fri Jun 25 08:31:52 2010 >>>> *Subject*: A PHD student using splice machine >>>> >>>> Dear Professor >>>> I'm a PHD student doing research in splice sites >>>> prediction >>>> and I have read your article"Splice Machine: predicting splice >>>> sites >>>> from high-dimensional local context representations". Now I want >>>> to do >>>> some comparisons on NN269 acceptor datasets, but I don't know >>>> how to >>>> use the software(how to do prediction). Would you like to tell >>>> me the >>>> details? >>>> Best wishes to you and your family! >>>> Thanks a lot! >>>> >>>> >>>> Yours sincerely >>>> Kang xuejiao >>>> >>>> >>> >>> >>> -- >>> ================================================================== >>> >>> Michiel Van Bel >>> PhD student >>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>> 3313809 >>> VIB Department of Plant Systems Biology, Ghent University >>> Technologiepark 927, 9052 Gent, BELGIUM >>> mibel@psb.vib-ugent.be >>> http://www.psb.vib-ugent.be >>> http://bioinformatics.psb.ugent.be >>> ================================================================== >>> >>> >>> >> >> >> > > > -- > ================================================================== > Michiel Van Bel > PhD student > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > mibel@psb.vib-ugent.be > http://www.psb.vib-ugent.be > http://bioinformatics.psb.ugent.be > ================================================================== > >
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ====================================================================== ------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere
Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ======================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
can you mail it again to this address? thaaaaaaaaanx On 06/28/2010 01:05 PM, Frederik Delaere wrote:
I mailed you a map of a hidden treasure
marijn wrote:
presents, you say?
On 06/28/2010 12:58 PM, Kenny Billiau wrote:
I bet he gets loads of presents this way ..
On Mon, 28 Jun 2010, Frederik Delaere wrote:
born the 24th of july 1984 ?
Kenny Billiau wrote:
and don't you just love their very descriptive email address .. ;)
On Mon, 28 Jun 2010, Frederik Delaere wrote:
looks like the average help request mail overhere :)
Michiel Van Bel wrote:
> *sigh* > sometimes I really want to tell those guys to > a) follow a decent english course > b) read the fucking manual > > I mean, it's not that difficult to read your email again before you > send > it, and make sure it makes sense :-( > > > ---------------------------- Original Message > ---------------------------- > Subject: Re:Re: Fw: A PHD student using splice machine > From: ¿µÑ©æ¯<kxj19840724@126.com> > Date: Sun, June 27, 2010 4:14 am > To: "Michiel Van Bel"<michiel.vanbel@psb.vib-ugent.be> > -------------------------------------------------------------------------- > > > > Dear Michiel > Thanks for your help! > I have tried to predict my test file using the software > but the > annotation file can be downloaded,why? > > Best regards! > > Xuejiao > > > > > > > >> ok, >> the software available on the website is only trained for >> Arabidopsis >> and Human. >> So you can only use a test-file (in fasta format). The >> output-format is >> described here: >> http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/ >> >> In order to train splicemachine yourself, you'll have to use the >> offline >> installation (see attachment). >> However, as I didn't write the software, I do not think I can >> really >> help you any further with any questions considering training >> splicemachine yourself. Please have a look at the pdf-files >> included in >> the attachment, for any further instructions. >> >> Michiel >> >> >> >> >> ¿µÑ©æ¯ wrote: >> >> >>> Hi Michieal >>> Thanks for your reply! >>> Here I want to know how to run the software.To the inputing >>> file, how >>> to distinguish the training file and the testing file?or the >>> all the >>> data should be in one file?Then how to distinguish the true or >>> false >>> sites? >>> Thanks a lot! >>> Regards! >>> Xuejiao >>> >>> >>> >>> >>>> Hi Kang, >>>> you can run the splicemachine software at this location: >>>> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >>>> >>>> Just copy-paste the sequences in fasta format into the >>>> text-field, and >>>> press the "run splicemachine" button. >>>> >>>> kind regards, >>>> Michiel >>>> >>>> >>>> >>>> Yves Van De Peer wrote: >>>> >>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> *From*: ¿µÑ©æ¯<kxj19840724@126.com> >>>>> *To*: yves.vandepeer@psb.vib-ugent.be >>>>> <yves.vandepeer@psb.vib-ugent.be> >>>>> *Sent*: Fri Jun 25 08:31:52 2010 >>>>> *Subject*: A PHD student using splice machine >>>>> >>>>> Dear Professor >>>>> I'm a PHD student doing research in splice sites >>>>> prediction >>>>> and I have read your article"Splice Machine: predicting splice >>>>> sites >>>>> from high-dimensional local context representations". Now I want >>>>> to do >>>>> some comparisons on NN269 acceptor datasets, but I don't know >>>>> how to >>>>> use the software(how to do prediction). Would you like to tell >>>>> me the >>>>> details? >>>>> Best wishes to you and your family! >>>>> Thanks a lot! >>>>> >>>>> >>>>> Yours sincerely >>>>> Kang xuejiao >>>>> >>>>> >>>>> >>>>> >>>> -- >>>> ================================================================== >>>> >>>> Michiel Van Bel >>>> PhD student >>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>> 3313809 >>>> VIB Department of Plant Systems Biology, Ghent University >>>> Technologiepark 927, 9052 Gent, BELGIUM >>>> mibel@psb.vib-ugent.be >>>> >>>> > http://www.psb.vib-ugent.be > > >>>> http://bioinformatics.psb.ugent.be >>>> ================================================================== >>>> >>>> >>>> >>>> >>>> >>> >>> >> -- >> ================================================================== >> Michiel Van Bel >> PhD student >> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> mibel@psb.vib-ugent.be >> http://www.psb.vib-ugent.be >> http://bioinformatics.psb.ugent.be >> ================================================================== >> >> >> >> > > > > ------------------------------------------------------------------------ > > > > Dear Michiel > Thanks for your help! > I have tried to predict my test file using the software > but the > annotation file can be downloaded,why? > > Best regards! > > Xuejiao > > > >> ok, >> the software available on the website is only trained for >> Arabidopsis >> and Human. >> So you can only use a test-file (in fasta format). The >> output-format is >> described here: >> http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/ >> >> In order to train splicemachine yourself, you'll have to use the >> offline >> installation (see attachment). >> However, as I didn't write the software, I do not think I can >> really >> help you any further with any questions considering training >> splicemachine yourself. Please have a look at the pdf-files >> included in >> the attachment, for any further instructions. >> >> Michiel >> >> >> >> >> ¿µÑ©æ¯ wrote: >> >>> Hi Michieal >>> Thanks for your reply! >>> Here I want to know how to run the software.To the inputing >>> file, how >>> to distinguish the training file and the testing file?or the >>> all the >>> data should be in one file?Then how to distinguish the true or >>> false >>> sites? >>> Thanks a lot! >>> Regards! >>> Xuejiao >>> >>> >>> >>>> Hi Kang, >>>> you can run the splicemachine software at this location: >>>> http://bioinformatics.psb.ugent.be/webtools/splicemachine/ >>>> >>>> Just copy-paste the sequences in fasta format into the >>>> text-field, and >>>> press the "run splicemachine" button. >>>> >>>> kind regards, >>>> Michiel >>>> >>>> >>>> >>>> Yves Van De Peer wrote: >>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> *From*: ¿µÑ©æ¯<kxj19840724@126.com> >>>>> *To*: yves.vandepeer@psb.vib-ugent.be >>>>> <yves.vandepeer@psb.vib-ugent.be> >>>>> *Sent*: Fri Jun 25 08:31:52 2010 >>>>> *Subject*: A PHD student using splice machine >>>>> >>>>> Dear Professor >>>>> I'm a PHD student doing research in splice sites >>>>> prediction >>>>> and I have read your article"Splice Machine: predicting splice >>>>> sites >>>>> from high-dimensional local context representations". Now I want >>>>> to do >>>>> some comparisons on NN269 acceptor datasets, but I don't know >>>>> how to >>>>> use the software(how to do prediction). Would you like to tell >>>>> me the >>>>> details? >>>>> Best wishes to you and your family! >>>>> Thanks a lot! >>>>> >>>>> >>>>> Yours sincerely >>>>> Kang xuejiao >>>>> >>>>> >>>>> >>>> >>>> -- >>>> ================================================================== >>>> >>>> Michiel Van Bel >>>> PhD student >>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>> 3313809 >>>> VIB Department of Plant Systems Biology, Ghent University >>>> Technologiepark 927, 9052 Gent, BELGIUM >>>> mibel@psb.vib-ugent.be >>>> http://www.psb.vib-ugent.be >>>> http://bioinformatics.psb.ugent.be >>>> ================================================================== >>>> >>>> >>>> >>>> >>> >>> >>> >> >> -- >> ================================================================== >> Michiel Van Bel >> PhD student >> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> mibel@psb.vib-ugent.be >> http://www.psb.vib-ugent.be >> http://bioinformatics.psb.ugent.be >> ================================================================== >> >> >> > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > Binari Implicitly Neglects All Recursive Iterations > https://maillist.psb.ugent.be/mailman/listinfo/binari > >
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ====================================================================== ------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Frederik Delaere
Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ====================================================================== Kenny Billiau Bioinformatics Group / GoFORSYS Scientific Programmer +49 331 567 8626 billiau@mpimp-golm.mpg.de Max Planck Institute for Molecular Plant Physiology Am Mühlenberg 1, 14476 Potsdam-Golm, Germany http://bioinformatics.mpimp-golm.mpg.de http://www.goforsys.de ======================================================================
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
------------------------------------------------------------------------
_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- ================================================================== Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde@psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== "Fat bottomed girls, you make the rockin' world go round." --F. Mercury
participants (5)
-
Frederik Delaere -
Kenny Billiau -
marijn -
Marijn Vandevoorde -
Michiel Van Bel