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Fwd: question concerning annotations based on motif recognition

Pascale Gaudet pgaudet at northwestern.edu
Wed Mar 7 06:35:47 PST 2007


I often rerun the analysis myself and if it seems convincing, I either use 
InterPro/Pfam as the "with", assuming the tool they have used must be 
comparable; otherwise sometimes do not annotate at all or contact the 
authors to find out how they have made the assessment.


Pascale


At 07:42 PM 3/6/2007 -0800, Karen Christie wrote:
>Hi,
>
>I would not use RCA for this. This is certainly not similar to the type of 
>analyses that prompted SGD to request the RCA code. The Evidence Code 
>Committee does still need to reconsider what RCA should be for, but I 
>don't think this should be in RCA.
>
>If you think this is a sequence similarity method, then we agreed at the 
>GOC to go with the Evidence Code Committee's recommendation to revert the 
>Annotation Camp's decision to use RCA instead of ISS for INterPro based 
>sequence similarity methods that are reviewed by curators. INstead, we 
>agreed to go with the ECC's recommendation that purely ISS based methods 
>should be ISS when curator reviewed or IEA when not.
>
>Alternatively, if you feel that there is not enough in the paper to use 
>ISS and you choose to annotate it, then I think you're left with NAS 
>because you are annotating an author statement that is not traceable to a 
>different reference.
>
>-Karen
>
>
>
>On Tue, 6 Mar 2007, Tanya Berardini wrote:
>
>>Am forwarding this on behalf of Chris, another curator here at 
>>TAIR.  We'd appreciate your thoughts.
>>
>>Tanya
>>
>>
>>Begin forwarded message:
>>
>>>From: "Christophe Tissier" <christophetissier at gmail.com>
>>>Date: March 6, 2007 4:50:02 PM PST
>>>To: "Tanya Berardini" <tberardi at acoma.stanford.edu>
>>>Subject: Fwd: question concerning annotations based on motif recognition
>>>hey, did you ever receive this email through the discussion group? I 
>>>never received a single answer!
>>>Chris
>>>---------- Forwarded message ----------
>>>From: Christophe Tissier <christophetissier at gmail.com>
>>>Date: Mar 2, 2007 10:35 AM
>>>Subject: question concerning annotations based on motif recognition
>>>To: annotation at genome.stanford.edu
>>>Hi,
>>>should we annotate to motif? For example, I have a paper with ATP- and 
>>>GTP-binding motifs. Often when these results are presented no specific 
>>>method is given as they are often considered common knowledge. Should we 
>>>annotate and if so, to what? I guess RCA might fit the bill, it is 
>>>afterall based on sequence alignments.
>>>Thanks your help
>>>Christophe
>>>-- Dr Christophe Tissier                                   MetaCyc: 
>>>http://www.metacyc.org/
>>>MetaCyc/TAIR Curator                                 AraCyc: 
>>>http://www.arabidopsis.org/tools/aracyc/
>>>Carnegie Institution of Washington                tel  +1 650 325 1521 x267
>>>Stanford University                                      fax +1 650 325 6857
>>>Stanford, CA94305
>>>USA
>>>-- Dr Christophe Tissier                                   MetaCyc: 
>>>http://www.metacyc.org/
>>>MetaCyc/TAIR Curator                                 AraCyc: 
>>>http://www.arabidopsis.org/tools/aracyc/
>>>Carnegie Institution of Washington                tel  +1 650 325 1521 x267
>>>Stanford University                                      fax +1 650 325 6857
>>>Stanford, CA94305
>>>USA





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