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Querying blast and getting raw hit fasta sequence

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.

blast sequence alignment
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updated by Ram Ram • written by ishengomae ishengomae

1 answer

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

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updated by Ram Ram • written by 5heikki 5heikki

Done. Thanks very much.

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written by ishengomae ishengomae

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