bij u thabe of bij mij???
L.
-------- Original Message --------
Hi Lieven,
I onece more cannot save coordinates of a gene moeld edited in Artemini.
I need to save the following coordinates for the gene Esi0031_0121:
650149..650208,650956..651132,651761..651904,652788..652932,653394..653455,654128..654328,654791..654934,655760..655847,662896..663023,663661..663789,664631..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510
When I put them to the respective widow and press "OK", the following
error announcement appears:
Cannot apply changes because of location error: Parse error at this
point:
..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510)): garbage at the end of the location
string
Could you, please, have a look on this?
Thanks,
Marek
Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
> Hi Marek,
>
> I tried it myself and I think it's due to the size of the scaffold. It is
> to big to be displayed on a page (it also happens with other large
> scaffolds apparently).
> We see how we can work around it.
>
> sorry and thanks for noticing this,
> best regards,
> lieven
>
>
>> Hi Lieven,
>>
>> I am not able to download the nucleotide sequence of the supercontig
>> sctg_0. After clicking on the hyperlink "F" in the BLAST output the
>> sequence cannot be downloaded and the browser replies with an error
>> message. However, other supercontig sequences can be displayed by
>> clicking on the corresponding hyperlink on the very same BLAST output
>> page. I do not understand at all what is going on.
>> Thanks,
>> Marek
>>
>> Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
>>
>>> Hi Marek,
>>>
>>> This is interesting information!
>>> I'm (our lab is) not responsible for producing the sequence, that job is
>>> done by GenoScope.
>>>
>>> The best you can do for the moment is report these kind of information
>>> on
>>> the wiki-page or in the structure comment field on the edit page
>>> (preferably in both :-) ).
>>> If the sequences is missing (Ns) than there is nothing much we can do
>>> (have you tried searching the Ectsi_Inf2kb blast database? maybe the
>>> missign piece is presen but not assembled into a larger contig??).
>>> If you notice that a gene has been 'split' over two contigs, we can
>>> report
>>> this to the sequencing center and they can use it for making a next
>>> assembly.
>>>
>>> grtz,
>>> lieven
>>>
>>>
>>>> Hi Lieven,
>>>>
>>>> I really highly appreciate your prompt assistance. I will probably
>>>> never cease having additionals troubles - here is another such: what
>>>> shoul I do if I found that it is impossible to create the correct gene
>>>> model because the underlying genome sequence is incomplete? Or even
>>>> worse, what to do with genes split into two separate supercontigs? For
>>>> example the models Esi0169_0001 and Esi0169_0002 on the very beginning
>>>> of the supercontig sctg_169 actually represent fragments of a signle
>>>> gene, whose intial exon is not repesented on the supercontig but seems
>>>> to reside near the 3' end of the small supercontig sctg_945. You
>>>> probably do not have any data linking these supercontigs together but
>>>> I have very good reasons to believe that they belong together, because
>>>> the gene is very vell conserved and the two pieces encoded by the two
>>>> supercontigs fit into the expected structure of the gene. How should I
>>>> annotate the gene?
>>>> Thanks,
>>>> Marek
>>>>
>>>> Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
>>>>
>>>>> Hi Marek,
>>>>>
>>>>> This is a not so easy issue (for us! not for you).
>>>>> the best option would be to select the model labeled 'CDS' and then
>>>>> insert
>>>>> your new coordinates. The other models you can ignore.
>>>>>
>>>>> grtz,
>>>>> lieven
>>>>>
>>>>>> Hi Lieven,
>>>>>>
>>>>>> thanks for the comments, it now seems that he problem with saving the
>>>>>> changes of gene models has been solved. I am sorry, however, to say
>>>>>> that I have just encountered another point requiring a discussion
>>>>>> with
>>>>>> you. I found that some genes I am annotating are incorrectly
>>>>>> predicted
>>>>>> as two or even three independent loci. How to correct these
>>>>>> instances?
>>>>>> Should I merge somehow the models into one, which I subsequetly
>>>>>> modify
>>>>>> bu inserting correct coordinates? If yes, how should I do it? Or
>>>>>> should I simply insert the correct coordinates into a field of one of
>>>>>> the partial "submodels" and ignore or delete the remaining?
>>>>>> Thanks,
>>>>>> Marek
>>>>>>
>>>>>> Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
>>>>>>
>>>>>>> Hi Marek,
>>>>>>>
>>>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no?
>>>>>>> I can see that you made an edit in the DB, but the problem is that
>>>>>>> there
>>>>>>> seems to be a double save. If you check in the history the last-1
>>>>>>> date
>>>>>>> you'll see your edit.
>>>>>>>
>>>>>>> We are sorting this out as quickly as possible.
>>>>>>>
>>>>>>> best regards,
>>>>>>> lieven
>>>>>>>
>>>>>>>
>>>>>>>> Dear Lieven,
>>>>>>>>
>>>>>>>> thanks for the change in artemini, this is exactly what I think
>>>>>>>> will
>>>>>>>> make the annotation much more straightforward. I checked the system
>>>>>>>> with one gene (correcting coordinates of one exon). I saved the
>>>>>>>> modified coordinates using "Save to server" command in "File" menu
>>>>>>>> option, but the model has not changed in the database yet. Are you
>>>>>>>> reviewing opur annotations before incorporating them into the
>>>>>>>> database? Or what is going on?
>>>>>>>> Thanks. Cheers,
>>>>>>>>
>>>>>>>> Marek
>>>>>>>>
>>>>>>>> Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
>>>>>>>>
>>>>>>>>> Dear Marek,
>>>>>>>>>
>>>>>>>>> we made some adjustments to the artemini functionality and as a
>>>>>>>>> result
>>>>>>>>> the
>>>>>>>>> coordinates you see in the artemini window are now the same as in
>>>>>>>>> the
>>>>>>>>> webpage (= they are in reference to the whole scaffold).
>>>>>>>>> You can just copy and paste your coordinates into the artemini,
>>>>>>>>> save
>>>>>>>>> it
>>>>>>>>> and they will be entered into the DB.
>>>>>>>>>
>>>>>>>>> I hope this can satisfy your needs. If not, please do let me know,
>>>>>>>>> so
>>>>>>>>> we
>>>>>>>>> can think of better solution.
>>>>>>>>>
>>>>>>>>> thanks and best regards,
>>>>>>>>> lieven
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---------------------------- Original Message
>>>>>>>>> ----------------------------
>>>>>>>>> Subject: Re: Ectocarpus proteins
>>>>>>>>> From: "Lieven Sterck" <lieven.sterck@psb.ugent.be>
>>>>>>>>> Date: Thu, November 8, 2007 11:17 pm
>>>>>>>>> To: melias@natur.cuni.cz
>>>>>>>>> Cc: cock@sb-roscoff.fr
>>>>>>>>> beg-bogas@psb.ugent.be
>>>>>>>>> --------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> Dear Marek,
>>>>>>>>>
>>>>>>>>> You can find a manual on how to use the artemis tool on the Sanger
>>>>>>>>> Institute website.
>>>>>>>>> May I inquire if you find the artemis tool itself not
>>>>>>>>> user-friendly
>>>>>>>>> or
>>>>>>>>> rather the way it is incoporated in the portal?
>>>>>>>>>
>>>>>>>>> The coordinates in the artemini view differ indeed from the ones
>>>>>>>>> on
>>>>>>>>> the
>>>>>>>>> webpage. this is because the sequence you get to see in the
>>>>>>>>> artemini
>>>>>>>>> view
>>>>>>>>> is only a subpart of the whole scaffold (this in order to let the
>>>>>>>>> procedure go faster). The coordinates you see in artemini are in
>>>>>>>>> reference
>>>>>>>>> to the subpart while you have (and also on the webpage) them in
>>>>>>>>> reference
>>>>>>>>> of the whole scaffold.
>>>>>>>>>
>>>>>>>>> In theory it is possible to make the coordinates 'box' editable.
>>>>>>>>> but,
>>>>>>>>> ...
>>>>>>>>> i'm a little bit reluctant to do this due to bad experience with
>>>>>>>>> this
>>>>>>>>> approach in previous projects. We noticied it is very easy to
>>>>>>>>> include
>>>>>>>>> mistakes this way (aspecially for non experienced annotators).
>>>>>>>>> That
>>>>>>>>> is
>>>>>>>>> why
>>>>>>>>> we include the artemini system in this version (where some basic
>>>>>>>>> checks
>>>>>>>>> on
>>>>>>>>> the structure are performed and you have the visual check of the
>>>>>>>>> structure).
>>>>>>>>> But I also completely understand your point that for more
>>>>>>>>> experienced
>>>>>>>>> users this might not be ideal...
>>>>>>>>> What we also can do is to add a function in the artemini to
>>>>>>>>> 'transfer'
>>>>>>>>> the
>>>>>>>>> coordinates you enter (in reference of the whole scaffold) onto
>>>>>>>>> the
>>>>>>>>> subpart in artemini. That way you could just paste your
>>>>>>>>> coordinates
>>>>>>>>> into
>>>>>>>>> the coordinate box of artemini, push the 'transfer' button and
>>>>>>>>> they
>>>>>>>>> will
>>>>>>>>> be adjusted onto the subpart. You can then also profit from the
>>>>>>>>> visual
>>>>>>>>> check. When you then save your modifications they will be entered
>>>>>>>>> to
>>>>>>>>> the
>>>>>>>>> DB.
>>>>>>>>> Do you think this might be more useful? or does it still sounds to
>>>>>>>>> much
>>>>>>>>> of
>>>>>>>>> a hastle?
>>>>>>>>>
>>>>>>>>> best and thanks for the feedback,
>>>>>>>>> lieven
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Dear Lieven,
>>>>>>>>>>
>>>>>>>>>> thanks for the link, I have successfully downloaded the protein
>>>>>>>>>> database. I would like to start making corrections of the gene
>>>>>>>>>> models
>>>>>>>>>> I
>>>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is
>>>>>>>>> there
>>>>>>>>> any
>>>>>>>>> manual how to work with the Artemini tool? I found it not be too
>>>>>>>>> user-friendly. For instance, I do not understand why the exon
>>>>>>>>> coordinates indicated by Artemini differs from the actual
>>>>>>>>> coordinates
>>>>>>>>> on
>>>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present
>>>>>>>>>> coordinates, with an incorrect first exon, are as follows:
>>>>>>>>>>
>>>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171
>>>>>>>>>>
>>>>>>>>>> I would like to change the first exon so that the coordinates are
>>>>>>>>>> like
>>>>>>>>> this:
>>>>>>>>>>
>>>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171
>>>>>>>>>>
>>>>>>>>>> The coordinates given for this gene in Artemini are as follows:
>>>>>>>>>>
>>>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296
>>>>>>>>>>
>>>>>>>>>> Why there is the difference? I have to say that I would highly
>>>>>>>>>> appreciate if it is possible to edit gene models just by typing
>>>>>>>>>> the
>>>>>>>>> correct coordinates of exons I found by comparing my CDS models
>>>>>>>>> with
>>>>>>>>> the
>>>>>>>>> contig sequence. Is this possible?
>>>>>>>>>> Thank you and best regards,
>>>>>>>>>>
>>>>>>>>>> Marek E.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Cituji Lieven Sterck <lieven.sterck@psb.ugent.be>:
>>>>>>>>>>
>>>>>>>>>>> Dear Marek,
>>>>>>>>>>> the download is available from this address:
>>>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus
>>>>>>>>>>> (login/passw : psbguest/ectocarpus)
>>>>>>>>>>> Apologises that I haven't informed you earlier, it is quite
>>>>>>>>>>> hectic
>>>>>>>>>>> for
>>>>>>>>> the
>>>>>>>>>>> moment.
>>>>>>>>>>> please let me know if this doesn't work.
>>>>>>>>>>> best regards,
>>>>>>>>>>> lieven
>>>>>>>>>>>> Dear Lieven,
>>>>>>>>>>>> you mentioned that from this week's Monday the whole predicted
>>>>>>>>> proteome of Ectocarpus should be available for download. I tried
>>>>>>>>> to
>>>>>>>>> find
>>>>>>>>> a
>>>>>>>>> link to the file at BOGAS web page but haven't found any. Could
>>>>>>>>> you,
>>>>>>>>> please, let me know, where to go for the downloading?
>>>>>>>>>>>> Thanks, best regards,
>>>>>>>>>>>> Marek Elias
>>>>>>>>>>>> Cituji lieven sterck <lieven.sterck@psb.ugent.be>:
>>>>>>>>>>>>> Dear Marek,
>>>>>>>>>>>>> From monday on you will be able to download all predicted
>>>>>>>>>>>>> protein/genes
>>>>>>>>>>>>> in batch.
>>>>>>>>>>>>> sorry for the delay.
>>>>>>>>>>>>> regards,
>>>>>>>>>>>>> lieven
>>>>>>>>>>>>> Kenny Billiau wrote:
>>>>>>>>>>>>>> -------- Original Message --------
>>>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal
>>>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100
>>>>>>>>>>>>>> From: melias@natur.cuni.cz
>>>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau@psb.ugent.be>
>>>>>>>>>>>>>> References:
>>>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s@www.natur.cuni.cz>
>>>>>>>>>>>>>> <472B0B6C.8060706@psb.ugent.be>
>>>>>>>>>>>>>> Hi Kenny,
>>>>>>>>>>>>>> thanks for the advice with getting the access to the
>>>>>>>>>>>>>> Ectocarpus
>>>>>>>>> portal. I have created an accounted and started to work. Is it
>>>>>>>>> possible to download the set of predicted protein sequences? It
>>>>>>>>> would suit me better to do some local stand-alone searches
>>>>>>>>> (BLAST,
>>>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks
>>>>>>>>>>>>>> again,
>>>>>>>>>>>>>> Marek
>>>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau@psb.ugent.be>:
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own
>>>>>>>>> login/password. You can use this login to access the ectocarpus
>>>>>>>>> wiki
>>>>>>>>>>>>>>> as
>>>>>>>>>>>>>>> well,
>>>>>>>>>>>>>>> Kenny
>>>>>>>>>>>>>>> melias@natur.cuni.cz wrote:
>>>>>>>>>>>>>>>> Dear Dr. Billiau,
>>>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark
>>>>>>>>>>>>>>>> Cock
>>>>>>>>>>>>>>>> sent
>>>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation
>>>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password
>>>>>>>>>>>>>>>> to
>>>>>>>>>>>>>>>> the
>>>>>>>>> portal. I have one to the BLAST page at the Ghent web site
>>>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work
>>>>>>>>> for the portal at
>>>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May
>>>>>>>>>>>>>>>> be
>>>>>>>>>>>>>>>> this
>>>>>>>>> is not the right link to the portal, so please, let me know how
>>>>>>>>> can
>>>>>>>>> I
>>>>>>>>> access the portal so taht I can start annotating. Thank
>>>>>>>>> you in advance and best regards,
>>>>>>>>>>>>>>>> Marek Elias
>>>>>>>>>>>>>>>> Department of Botany
>>>>>>>>>>>>>>>> Faculty of Science
>>>>>>>>>>>>>>>> Charles University
>>>>>>>>>>>>>>>> Benatska 2
>>>>>>>>>>>>>>>> 128 01 Praha 2
>>>>>>>>>>>>>>>> Czech Republic
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> ==================================================================
>>>>>>>>> Kenny Billiau
>>>>>>>>>>>>>>> Web Developer
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>> kenny.billiau@psb.ugent.be
>>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be
>>>>>>>>> ==================================================================
>>>>>>>>>>>>> --
>>>>>>>>>>>>> ==============================================================
>>>>>>>>>>>>> Lieven
>>>>>>>>> Sterck Predoctoral fellow Tel:+32
>>>>>>>>> (0)9
>>>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department
>>>>>>>>> of
>>>>>>>>> Plant
>>>>>>>>> Systems Biology, UGent
>>>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division
>>>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium
>>>>>>>>>>>>> Email:
>>>>>>>>> lieven.sterck@psb.ugent.be
>>>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be
>>>>>>>>>>>>> --------------------------------------------------------------
>>>>>>>>>>>>> Algal
>>>>>>>>> Genetics Group
>>>>>>>>>>>>> UMR 7139 CNRS-UPMC
>>>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂégÃÂÃÂÃÂÃÂÃÂÃÂÃÂétaux
>>>>>>>>>>>>> Marins et
>>>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂécules (Marine
>>>>>>>>>>>>> Plants and
>>>>>>>>>>>>> Biomolecules)
>>>>>>>>> Station Biologique Place Georges Teissier, BP74
>>>>>>>>>>>>> 29682 Roscoff Cedex, France
>>>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html
>>>>>>>>>>>>> ==============================================================
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
--
==============================================================
Lieven Sterck Predoctoral fellow
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, UGent
Bioinformatics and Evolutionary Genomics Division
Technologiepark 927, B-9052 Gent, Belgium
Email: lieven.sterck@psb.ugent.be
Website: http://bioinformatics.psb.ugent.be
--------------------------------------------------------------
Algal Genetics Group
UMR 7139 CNRS-UPMC
Végétaux Marins et Biomolécules (Marine Plants and Biomolecules)
Station Biologique
Place Georges Teissier, BP74
29682 Roscoff Cedex, France
Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html
==============================================================