How to show the entire query sequence in the alignment in NCBI stand-alone blastn

Question

[urjaswita]

Hi folks,

I am using standalone blast and I want to see alignment summary like the one produced in the online version on ncbi website. Basically, I want to see where all my HSPs are aligning in the entire query sequence. But the stand alone version of blastn only shows local alignments between HSPs and the part of query. Any ideas how can I see the subject sequences aligned to the whole query sequence, and not just local alignments? I want to visualize the globally how much and which parts of query are aligned.

Thanks a lot for help!

[Santosh Anand]

Blast is a local alignment tool. Maybe you are looking for a global aligner. See my answer in this post How to force blastn to align full subject

Answer 1

[GenoMax]

You can't do this with BLAST @NCBI.

You could use Blast at Expasywhich displays results in a way you want to visualize them. Locally aligned HSP's mapped on a much longer "hit" . In this case parts of BRCA2 protein mapped against the entire BRCA2 protein (panel on the right, note blocks of color i.e. query chunks against full protein in gray).