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Re^3: Homologene BioPerl

by erix (Vicar)
on Dec 02, 2011 at 20:36 UTC ( #941432=note: print w/ replies, xml ) Need Help??


in reply to Re^2: Homologene BioPerl
in thread Homologene BioPerl

See also the NCBI explanatory files in:

ftp://ftp.ncbi.nih.gov/pub/HomoloGene

Especially the README file, which says:

---------------------------------------------------------- homologene.data is a tab delimited file containing the following columns: 1) HID (HomoloGene group id) 2) Taxonomy ID 3) Gene ID 4) Gene Symbol 5) Protein gi 6) Protein accession -----------------------------------------------------------

So yes, you search for your human accession in column 6, then look what value column 1 has (the homologene group id), and then look up whether there is a row which has both taxonomy_id=7227 (=D.melanogaster) *AND* that homologene group id.

Btw (if you want more data), the 'Gene ID' can be handy too as it gives you access to the whole of entrez, and lets you construct URL's into the main gene page, etc, etc. More data 'addressable' via 'gene id' in the files in:

ftp://ftp.ncbi.nih.gov/gene/DATA

(esp. gene_info and gene2accession)

(btw, I do /not/ see any Homologene records for your NP_001124398, so maybe your bioperl script does work after all, if you give it a human accession with known data in homologene)


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