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Old 07-27-2014, 11:12 AM   #1
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Default 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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Old 07-27-2014, 11:45 AM   #2
GenoMax
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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?
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Old 07-27-2014, 01:31 PM   #3
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Quote:
Originally Posted by GenoMax View Post
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?
Yes, gi# and accession with annotation is what I am looking for. But I could not locate them from the link that you send? Could you specify? Thank you GenoMax!

Last edited by favorite; 07-27-2014 at 01:48 PM.
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Old 07-27-2014, 05:00 PM   #4
GenoMax
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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:

Code:
$ 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]
Using
Code:
-entry all
is supposed to give you the entire contents.

Do you have a list of the gi's you are interested in? You could use that with the above command.
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Old 07-28-2014, 05:46 AM   #5
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Thank you GenoMax, this will do!
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