How to download GI number and locus tag number for organism?
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5.3 years ago
fernan23 • 0

Hi everyone,

Apologies for the naivety but I have a question about downloading data for subsequent GO annotation using Scaffold proteomics software.

I would like to download the list of GI numbers for an organism along with its corresponding locus tag or accession number as it is sometimes called. 

For example E. coli K12 http://www.ncbi.nlm.nih.gov/nuccore/NC_002695.1

has a total list of all genes with their GI and locus tags, but I can't download the entire list, it either gives me genome seqence or the genome GI number or accession number, not the numbers for each gene. Does anyone know if its possible to download a list with these two pieces of info. 

p.s. I have a file with locus tag and GO annotation from UniProt but my accession file used in Scaffold has GI numbers so my GO database has to also have GI numbers along with locus tags to work together.

D

GI locus tag scaffold proteomics GO Annotation • 4.0k views
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5.3 years ago

Take a look at the NCBI eutils

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5.3 years ago
5heikki 9.6k

For proteins with Entrez Direct:

esearch -db nuccore -query "NC_002695.1" | elink -target protein | efetch -format docsum | xtract -element Extra | tr "\t" "\n" | head
gi|359268811|ref|YP_004935383.1|
gi|229544783|ref|NP_308066.2|
gi|229544782|ref|NP_310110.2|
gi|229544781|ref|NP_310528.2|
gi|229544780|ref|NP_312006.2|
gi|229544779|ref|NP_312265.2|
gi|229544778|ref|NP_312824.2|
gi|229544777|ref|NP_313350.2|
gi|229544776|ref|NP_311809.3|
gi|162139821|ref|NP_308064.2|
..
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see above

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