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Originally posted by fefe89 View PostThank 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
Code:grep -m1 -w ^74664614 gi_taxid_prot.dmp
Code:awk '$1 == 74664614 {print;exit}' gi_taxid_prot.dmp
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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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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
Last edited by rhinoceros; 08-10-2014, 11:45 PM.
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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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