querying a database with a substring contained in a file fasta

Question

[marghe08]

Hello! I present my problem. I created with the command "makeblastdb" a database that contains my sequences of interest. Now I want to make a query: the file on which do the query (assume it's called NG_006672.fasta) contains a single sequence; I want to make a query on a substring of the sequence contained in my file, for example to take a substring of length 20. I would like to make a query being able to act on the indices of my query sequence

[GenoMax]

I would like to make a query being able to act on the indices of my query sequence.

Please clarify what you mean by this? This request does not match the first part of your question.

Answer 1

[shenwei356]

you can use tools like EMBOSS, seqtk and so on to retrieve subsequence and then blast.

e.g., use subseq (usage) of SeqKit:

• First 12 bases

  $ seqkit subseq -r 1:12 seqs.fa > subseq.fa
  

• Last 12 bases

  $ seqkit subseq -r -12:-1 seqs.fa > subseq.fa
  

• Subsequences without first and last 12 bases

  $ seqkit subseq -r 13:-13 seqs.fa > subseq.fa