This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Base by base alignment from BLAST to reference

Hi All,

I have aligned a 5k sequence to a reference sequence longer than 5k. The Blast alignment report shows alignment not from the start position of the reference but from bases from where alignment starts. I want an alignment report where reference which does not match to the consensus is also mentioned in the report.

For example (Desired Output);

Query      ~~~~~~~~~~  ~~~~~~~~~~ ~~~~~~~~~~  AGCTTGGCCC  ATTGCATACG  TTGTATCCAT 
Reference  AAACGAGCTC  TGCTTTTATA GGCGCCCACC  AGCTTGGCCC  ATTGCATACG  TTGTATCCAT

Query      ~~~~~~~~~~ ~~~~~~~~~ 
Reference  AATTAAGCGC GCAACGATG

Blast only reports bases which are aligned. Example:

Query     AGCTTGGCCC  ATTGCATACG  TTGTATCCAT 
Reference AGCTTGGCCC  ATTGCATACG  TTGTATCCAT

I can only use BLAST to do this.

How can I obtain such alignment report using Blast?

Thanks in advance!!!

blast alignment
• 1,471 views • link
updated by h.mon h.mon • written by kspata kspata

1 answer

Blast is a local alignment tool, which means it won't do what you want. You can play with gap and indel opening and extension parameters and try your luck. References:

Unable to blast entire coding sequence of gene

Force blast to align the whole query read

• 1 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this