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-   -   Identifying gene name synonyms (http://seqanswers.com/forums/showthread.php?t=7602)

Jordy224 10-29-2010 10:21 PM

Identifying gene name synonyms
 
A quick question.
Using Entez database or AmiGO, How to you find all synonyms of a particular gene in other genomes without falling back on a sequence homology search.

For example. Gene psaB can also be annotated as ycf4.

In fact, I am attempting to identify protein clusters between my newly sequenced genome and the relatives using a script. So, I need to obtain a list of all synonyms.

Whats the best method, or software.

RockChalkJayhawk 11-01-2010 09:03 AM

Quote:

Originally Posted by Jordy224 (Post 28192)
A quick question.
Using Entez database or AmiGO, How to you find all synonyms of a particular gene in other genomes without falling back on a sequence homology search.

For example. Gene psaB can also be annotated as ycf4.

In fact, I am attempting to identify protein clusters between my newly sequenced genome and the relatives using a script. So, I need to obtain a list of all synonyms.

Whats the best method, or software.

Have you tried HomoloGene?

Jordy224 11-02-2010 05:50 PM

I currently use the protein cluster application in NCBI
For example:

http://www.ncbi.nlm.nih.gov/proteinclusters/624653

Notice there are multiple names for this single protein, and yet the proteins are homologous. This is just a fact of annotation by the authors.

It should be possible to compare genomes by protein name as in present or absent without need for time-consuming homology search.

ntremblay 11-30-2010 02:05 PM

Hi,

try using this tool: http://idconverter.bioinfo.cnio.es/IDconverter.php

it's very good to convert various ID's, give you the result on screen or txt/excel file and you can chose wich database you want to cross-reference,

Joann 12-01-2010 07:56 AM

thanks for the tool site
 
Quote:

Originally Posted by ntremblay (Post 30455)
Hi,

try using this tool: http://idconverter.bioinfo.cnio.es/IDconverter.php

it's very good to convert various ID's, give you the result on screen or txt/excel file and you can chose wich database you want to cross-reference,

Hi,
Thanks for the tool site. As an ongoing project, I've been trying to work up a non-specialty paper for biologists titled "How to get your text mined" and one of my suggestions is going to be use of the NCBI unique gene id number within the text of any article for publication.


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