[Biopython] alignment/matching algorithm whichs allows missmatches at certain positions

[Brad Chapman]

Hi Stefanie;

> Does someone knows an algorithm to search for sequence similarity by allowing missmatches at certain positions?
> 
> E.g.
> Looking in a sequence database for 
> 
> ATGCTCGCGCTCGCTCGCGCA
> 
> by allowing an missmatch at position [3] and [18].

dreg and fuzznuc in EMBOSS both do this:

http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/dreg.html
http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/fuzznuc.html

The SHRiMP aligner also allows you to specify a seed with defined
match and mismatch positions:

http://compbio.cs.toronto.edu/shrimp/

See the '-s' option in the README.

Hope this helps,
Brad