How to use Blastp one sequence vs fasta file and get most similar sequence?

Question

[Bioinformatics_begginner]

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.

[Ram]

Why do you want to do it in python?

[Bioinformatics_begginner]

can be in shell commands too. I said python but not mandatory to be on python

[Ram]

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.

[Bioinformatics_begginner]

Thank you and sorry but could you detail more? I understand i build a local database makeblastdb -in {bacteria_clusters} -dbtype prot -out Bacteria_db then how can I run blastp with my file vs Bacteria_db and get the most similiar

[Ram]

Please read the blast manual. You're already halfway there, I'm confident you can figure this out yourself.

Answer 1

[Bioinformatics_begginner]

okay here is the solution. Thank you for your help Ram .

blastp -outfmt 7 \
-db database \
 -query file \
  > table.tsv

[GenoMax]

Use -out filename instead of using >.

[Ram]

Please accept your own answer to provide closure to the post.