Question: How to show the entire query sequence in the alignment in NCBI stand-alone blastn
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gravatar for urjaswita
2.9 years ago by
urjaswita90
United States
urjaswita90 wrote:

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!

blast sequence alignment ncbi • 1.6k views
ADD COMMENTlink modified 2.9 years ago by genomax92k • written 2.9 years ago by urjaswita90
1

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Santosh Anand5.2k
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gravatar for genomax
2.9 years ago by
genomax92k
United States
genomax92k wrote:

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).

cap

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by genomax92k
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