Blast from accession number

fefe89 · 08-10-2014, 11:06 PM

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

rhinoceros · 08-10-2014, 11:32 PM

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

fefe89 · 08-10-2014, 11:44 PM

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

rhinoceros · 08-10-2014, 11:57 PM

Quote:

Originally Posted by fefe89

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.

fefe89 · 08-11-2014, 12:08 AM

Thank's again. It works perfectly

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08-10-2014, 11:06 PM	#1
fefe89 Member Location: italy Join Date: Jul 2014 Posts: 26	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

08-10-2014, 11:32 PM	#2
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	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 __________________ savetherhino.org Last edited by rhinoceros; 08-10-2014 at 11:45 PM.

08-10-2014, 11:44 PM	#3
fefe89 Member Location: italy Join Date: Jul 2014 Posts: 26	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

08-11-2014, 12:08 AM	#5
fefe89 Member Location: italy Join Date: Jul 2014 Posts: 26	Thank's again. It works perfectly