How to use Blastp one sequence vs fasta file and get most similar sequence?
Hello,
I have a protein sequence with format
record = SeqRecord(Seq(sequence), id=Protein_id, description=Protein_id, name=Protein_id)
And a .fasta file with different proteins and sequences (Bacteria.fasta)
I want to apply blastp record vs all the sequences in fasta and retrieve the most similiar sequence? (It is a local blastp against this local database)
How can I do this in python?
Best Regards and Thank you.
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Ram
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Bioinformatics_begginner •
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Bioinformatics_begginner •
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okay here is the solution. Thank you for your help Ram .
blastp -outfmt 7 \
-db database \
-query file \
> table.tsv
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Why do you want to do it in python?
can be in shell commands too. I said python but not mandatory to be on python
Write the sequence you have in memory to a file (unless you read it from a file, in which case just use that file) and run blastp on the command line, with makeblastdb if required.
Thank you and sorry but could you detail more? I understand i build a local database
makeblastdb -in {bacteria_clusters} -dbtype prot -out Bacteria_dbthen how can I run blastp with my file vs Bacteria_db and get the most similiarPlease read the blast manual. You're already halfway there, I'm confident you can figure this out yourself.