Alternative to BLAST with N and mismatches as input

Question

[gernophil]

Hey, I am looking for a good alternative to BLAST. BLAST is not really ideal for me, since I have Ns in my input and AFAIR BLAST doesn't accept these. Also I want to specify a number of mismatches and in BLAST I would need to play around with the word size and the gap penalty and stuff, but I just want to use sth. like --allowed-mismatches 5 or so. Also It would be great, if I could define a region within a sequence where these mismatches are allowed and others, where no mismatches are allowed. So, I need sth. that takes this as input

sequence: CGTAGCATCGATCGATCGATNT # N can be any base
mismatches: up to 5 in the first 10 bases, none in the last 10

and output any area in a reference FASTA that would match these criteria (like BLAST), not just one.

Does anyone know such an aligner?

[lieven.sterck]

I seem to remember that BLAST has no problem with Ns in the input sequences (nor the DB for that matter)

Also, keep in mind that BLAST is NOT an aligner tool, it's a search tool (sort of the google for sequences). Depending on your goals have a look a some of the real aligners (HiSAT, BBmap, ... tools like that or for instance the EMBOSS package for old school classic aligners)

Not sure if applicable for your situation but FASTA is a blast like tool (even older than blast), but I don't know it well enough to say if it can do what you want it to do.