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10-29-2010, 10:21 PM
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#1 |
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Junior Member
Location: VA,USA Join Date: Feb 2009
Posts: 7
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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. |
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11-01-2010, 09:03 AM
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#2 | |
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Senior Member
Location: Rochester, MN Join Date: Mar 2009
Posts: 191
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Quote:
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11-02-2010, 05:50 PM
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#3 |
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Junior Member
Location: VA,USA Join Date: Feb 2009
Posts: 7
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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. |
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11-30-2010, 02:05 PM
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#4 |
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Member
Location: Montreal, Quebec, Canada Join Date: Dec 2009
Posts: 30
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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, |
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12-01-2010, 07:56 AM
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#5 | |
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Senior Member
Location: Woodbridge CT Join Date: Oct 2008
Posts: 231
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thanks for the tool site
Quote:
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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