[Gofriends] Fw: Question

[Sorin Draghici]

Yes,  a bunch of comparisons in terms of accuracy of translation, speed and 
scope are included in:

Sorin Draghici, Sivakumar Sellamuthu, Purvesh Khatri. Babel's tower revisited: a 
universal resource for cross-referencing across annotation databases. 
Bioinformatics, 22(23):2934-2939, December 2006.

http://vortex.cs.wayne.edu/papers/Babel.tower.pdf

As a word of caution, I have just found out that the translations involving 
Swiss-Prot/Trembl, PIR, PDB are currently not working in our tool. That means 
our tools currently performs only 357 types translations out of it usual range 
of  462 translation types. This was caused by the fact that one of the databases 
we relied upon is not longer being maintained. It will take us a couple of weeks 
to redesign our database in order to go around this problem.

Regards,

Sorin


Sorin Draghici, Ph.D.


Associate Professor		Tel: (313) 577-5484
Dept. of Computer Science	Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall,
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/index.htm (personal)
WWW: http://vortex.cs.wayne.edu/Projects.htm (lab)


Suzanna Lewis wrote:
> Just out of curiosity. Has anyone compared the answers that these 
> various tools provide? Presumably (given organism constraints) they 
> should be consistent, but has this been checked?
> 
> -S
> 
> On May 15, 2008, at 4:05 AM, Judith Blake wrote:
> 
>> Dear Sudhindra,
>>
>> Yes MGI gives SwissProt IDs (now UniProtKB IDs)
>>
>> each gene report provides the UniProtKB ID for the representative 
>> protein for that gene.
>>
>> In addition, there is a nightly-refreshed ftp report that provides 
>> this information
>>
>> it can be found here:
>> ftp://ftp.informatics.jax.org/pub/reports/MRK_SwissProt_TrEMBL.rpt
>>
>> details about ftp reports provided by MGI are here
>> ftp://ftp.informatics.jax.org/pub/reports/index.html
>>
>> I hope this information is useful to you.
>>
>> Judy
>>
>>
>> Sudhindra.Gadagkar at notes.udayton.edu wrote:
>>>
>>> Does MGI give Swissprot IDs?
>>> Sudhindra Gadagkar
>>>
>>> ---------------------------------------------------------------------------- 
>>>
>>> Sudhindra R. Gadagkar, Ph.D.
>>> Department of Biology
>>> University of Dayton
>>> 300 College Park
>>> Dayton, OH 45469-2320
>>>
>>> Ph: (937) 229-2410
>>> Fax: (937) 229-2021
>>> Email: gadagkar at notes.udayton.edu
>>> ---------------------------------------------------------------------------- 
>>>
>>>
>>> "The aim of science is not to open the door to infinite wisdom, but 
>>> to set a limit to infinite error."
>>> - Bertolt Brecht, Life of Galileo
>>>
>>>
>>>
>>>
>>> ----- Forwarded by Sudhindra _ Gadagkar/A&S/FacStaff/UDayton on 
>>> 05/14/2008 10:48 PM -----
>>> *Paul Sternberg <pws at caltech.edu>*
>>> Sent by: gofriends-bounces at genome.stanford.edu
>>>
>>> 05/14/2008 08:43 PM
>>>
>>>     
>>> To
>>>     Milagros Perez <miperez at vbi.vt.edu>
>>> cc
>>>     gofriends at genome.stanford.edu
>>> Subject
>>>     Re: [Gofriends] Question
>>>
>>>
>>>
>>>     
>>>
>>>
>>>
>>>
>>>
>>> Milagros,
>>> What sort of genes?  If they are worm genes, then wormmart; if they  
>>> are mouse genes, MGI.... etc. etc.
>>> Paul
>>>
>>> On May 14, 2008, at 12:13 PM, Milagros Perez wrote:
>>>
>>> > I was hoping someone could help me with this:
>>> >
>>> > If I have a list of genes, is there any way to get their 
>>> respective  > swissprot IDs without having to do it manually? Does 
>>> anyone know of  > a website or software that offers that service?
>>> >
>>> > Thank you,
>>> >
>>> > Milagros Perez
>>> > _______________________________________________
>>> > Gofriends mailing list
>>> > Gofriends at geneontology.org
>>> > http://fafner.stanford.edu/mailman/listinfo/gofriends
>>>
>>> Paul Sternberg
>>> pws at caltech.edu
>>>
>>>
>>>
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>>
>>
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> 
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