Best Way To Get All Genes/Proteins Related To A Taxon Id From Metahit And Hmp

Question

[Dhruv Sakalley]

Hi, I have a list of taxid from species that are a part of MetaHIT and taxid from species that are a part of HMP database. But I am looking far a programmable way for obtaining all the gene ids, genes, gene symbols, gene description under these taxids. Some sample taxid's are : MetaHIT: 657324 717962 751585. HMP: 563193 411465 563194. If there is one dump file containing all this information that would be awesome.

Regards, Dhruv

Answer 1

[Pierre Lindenbaum]

You can find some genes for the human genome (see the table on the right):

• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606

but it seems that there is no sequences annotated as "Gene" in:

• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=657324
• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=717962
• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=751585
• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=563193
• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=411465
• http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=563194

If you want to find the sequences (!= gene) in those organisms, see this related question.