*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