Querying blast and getting raw hit fasta sequence

Question

[ishengomae]

I have downloaded refseq_rna database and I want to query this database on my standalone blast with tblastn. I have many queries and what I want to achieve is to not only get blast alignments but also to get the entire length of the hit sequences that produced the alignments. Can somebody suggest to me a simpler way of doing this? I am happy to elaborate further in case more clarification is needed.

Answer 1

[5heikki]

Parse the Subject IDs to a list and extract them from your db with blastdbcmd -entry_batch

[ishengomae]

Done. Thanks very much.