Question: Local Fasta Query Using List Of Gi Accessions
0
gravatar for User 5039
8.3 years ago by
User 50390
User 50390 wrote:

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 • 1.9k views
ADD COMMENTlink written 8.3 years ago by User 50390
1

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?

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 82k
1
gravatar for Niek De Klein
8.3 years ago by
Niek De Klein2.5k
Netherlands
Niek De Klein2.5k wrote:

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.

ADD COMMENTlink written 8.3 years ago by Niek De Klein2.5k
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