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Local Fasta Query Using List Of Gi Accessions

Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.

fasta blast
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updated by Niek De Klein Niek De Klein • written by User 5039 • User 5039

It is not clear what is it that you are trying to do. Do you want to align sequences identified by accession numbers to another sequence?

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written by Istvan Albert Istvan Albert

1 answer

You want to BLAST over the fasta file?

First make a database of your fasta file with this command: makeblastdb -in my_seqs.fasta -out my_seqs.fasta.

Then download all the fasta sequences of your GI list and save them in queryseq.fasta.

After that do blastp -query queryseq.fasta -db my_seqs.fasta -out result.txt if your query and database are protein sequences or blastn -query queryseq.fasta -db my_seqs.fasta -out result.txt if your query and database are nucleotide sequences.

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written by Niek De Klein Niek De Klein

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