How can I get the fasta sequences of BLASTP results
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7.1 years ago
tcf.hcdg ▴ 70

Hello 

I have a query sequence and did protein BLAST and get the 100 hits. Now iwant to get the sequence of these 100 hits. Is there any way I can get the sequence automatically instead of getting one by one? I use the option download fasta file but sequences are not in fasta file.

 

Thanks

blast fasta • 2.0k views
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Hi, 

First, when you select all your Hits and clic on "Download Fasta", files ARE in fasta format. The fasta format does not mean each time Nucleotide sequence. ;) 

So, a solution can be -> Find the CDS associated (in the description the CDS link is available) to your protein sequence and with his GENEID find the CDS nucleotide sequence. To achieve this, you can: 

  1. Script your requests and from the BLASTP matchs, extract the CDS (GENEID) and the nucleotide sequence.
  2. Do the stuff manually for each hit (100 it will be a little bit... fastidious).
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