Base by base alignment from BLAST to reference

Question

[kspata]

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!!!

Answer 1

[h.mon]

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