I need to map lots of IDs from different databases (TAIR, FlyBase, WormBase etc) to UniProt accession numbers. So far I've found 2 conversion tools, UniProts ID mapping and DAVID. I tried the mapping of TAIR to UniProt first, but of the 1849 sequences I put in only 180 mapped on UniProt and 118 on DAVID.
So I'm looking for better ID converters. Any suggestions?
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written
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Niek De Klein
1 answer
You could have a look at BridgeDB. It is intended for ID mapping. You can use it as a software framework in Java or install it as a local webservice and use it from whatever you prefer. It can use databases (ENSEMBL and HMDB based ones are provided) but you can make your own from downloaded tables, it can also use webservices like the ones you mentioned and even flatfiles. It can also stack files which is neat if you have your own ID system (eg for custom arrays). See also: http://dx.doi.org/10.1186/1471-2105-11-5
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I like using biomart http://central.biomart.org/
Duplicate of Gene ID conversion tool the most viewed question on BioStar, please use search.
Is it possible that those individual sources (TAIR, FlyBase, WormBase, etc) provide the best sources of mapping to UniProt? They might be the most motivated to do a good job and understand the species-specific challenges? Just a thought...
Might be, but in reality a lot of the mappings are provided by the UniProt and ENSEMBL curation teams. Of course they do evaluate mappings provided by other databases.