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More than likely you are going to have to do some work to get this information. I don't know of a file that has all gi/accession numbers (that doesn't mean there isn't one available somewhere).
I also thought of a second way. If you are interested in sequences in blast databases then you can use the following command (available in the blast+ package) to query the blast database and pull out the information you are looking for. I used 456346 as a "gi" example. (first number is gi, second number is accession, third entry is title)
For example:
UsingCode:$ blastdbcmd -db /path_to_database/nr -entry 456346 -outfmt "%g %a %t" 238236 AAB20203.1 transmembrane secretory component [Homo sapiens] 255098 AAB23176.1 transmembrane secretory component [Homo sapiens] 456346 CAA51532.1 Polymeric immunoglobulin receptor [Homo sapiens] 51476744 CAH18339.1 hypothetical protein [Homo sapiens]
is supposed to give you the entire contents.Code:-entry all
Do you have a list of the gi's you are interested in? You could use that with the above command.Leave a comment:
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NCBI Eutils may be of help. http://www.ncbi.nlm.nih.gov/books/NBK1058/
Are you interested in getting a list of gi# and corresponding accession?Leave a comment:
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is there a file of annotated names for NCBI sequence identifiers?
Hi Seqanswerers, I looked online but could not a file to link names to the NCBI sequence identifiers, examples below.
I can search on NCBI to get their name, for example, the first one will get "Synthetic Enterobacteria phage phiX174.1f, complete genome". But I can not do this manually for all of them. Are there a file that have 2 columns, one is the identifier and the other one is the annoted sequence information?
thanks much!!!
gi|410809623|gb|JX913857.1|
gi|397909638|gb|JQ764988.2|
gi|258548842|gb|GQ449188.1|
gi|397310634|gb|JQ839147.1|
gi|216089|gb|M14428.1|S13CG
gi|453201063|gb|JQ999043.1|
gi|474443144|dbj|AB627568.1|
gi|451172671|gb|KC335150.1|
gi|192792159|gb|EU794108.1|
gi|399935676|gb|JX095881.1|
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