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Old 08-10-2014, 11:06 PM   #1
fefe89
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Default Blast from accession number

Hey guys,

I have a list of all the genes I have with the respective GI and accession number.

What I would like to do is to make a blast using these accession number instead of the fasta sequence (as I ususally do with blast+), in order to have all the info (and particularly the taxonimy ID).

Is it possible? How can I do?

Thank you in advance
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Old 08-10-2014, 11:32 PM   #2
rhinoceros
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You don't need blast for connecting GI/Accession to Taxonomy ID. This file links Prot GI to TaxID and this file does the same with Nucl GIs. Alternatively, if you don't want to download the big map files, you can use e.g. Entrez Direct, for example:

Code:
esearch -db protein -query ProtGiNumber | elink -target taxonomy | efetch -format xml | xtract -element TaxId | cut -f1
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Last edited by rhinoceros; 08-10-2014 at 11:45 PM.
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Old 08-10-2014, 11:44 PM   #3
fefe89
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Thank you very much. It seems really perfect for my problem.

But, how can I work with that kind of file (dmp)?

Sorry but I'm really new of this world
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Old 08-10-2014, 11:57 PM   #4
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Quote:
Originally Posted by fefe89 View Post
Thank you very much. It seems really perfect for my problem.

But, how can I work with that kind of file (dmp)?

Sorry but I'm really new of this world
It's a tab separated text file. First column is Gi and second column is tax id. For example:

Code:
grep -m1 -w ^74664614 gi_taxid_prot.dmp
Looks for line in which first column is exactly 74664614 and prints the first (I think also only) occurrence. The same with awk:

Code:
awk '$1 == 74664614 {print;exit}' gi_taxid_prot.dmp
Also check the edit in my previous answer.
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Old 08-11-2014, 12:08 AM   #5
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Thank's again. It works perfectly
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