alignable portion of a genome

[fadista]

Hi,

I would like to know of a good and fast way that could help me calculate the alignable portion of a genome (not human), given a reference sequence.
When I say alignable portion I mean that I want to know all the positions of the genome that can be covered uniquely by reads of 36 bp and up to 2 mismatches.

Best regards,
João

[nilshomer]

Hi,

I would like to know of a good and fast way that could help me calculate the alignable portion of a genome (not human), given a reference sequence.
When I say alignable portion I mean that I want to know all the positions of the genome that can be covered uniquely by reads of 36 bp and up to 2 mismatches.

Best regards,
João

There are tools in BFAST (https://secure.genome.ucla.edu/index.php/BFAST) in the "butil" directory to solve exactly the problem described above. They include "bindexhist" and "bindexdist", which are documented in the accompanying reference manual.