Local Fasta Query Using List Of Gi Accessions

Question

[User 5039]

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.

[Istvan Albert]

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?

Answer 1

[Niek De Klein]

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.