Is there an algorithm that align two sequences?

[fahim]

Is there any algorithm that align two sequences just like Smith-Waterman where where the gaps are not allowed. Only mismatches are allowed.

I do know that this can be achieved using heavy penalty on insertion and deletion but was wondering if any dedicated algo exist.

[GenoMax]

Check into SSEARCH from the FASTA alignment package.

Lastz may also work: http://www.bx.psu.edu/~rsharris/lastz/

[westerman]

Sounds like you have the proper approach. S&W putting a large penalty on insert/deletes. But as always, take GenoMax's advice. He knows a lot!

[fahim]

Thanks GenoMax. Will look at it

[krobison]

BLAST 1.x!!!

I assume you are trying to align a lot of sequences; otherwise it is probably about a page of code in any modern programming language & a good exercise for a beginning student.

[cs]

Is there any algorithm that align two sequences just like Smith-Waterman where where the gaps are not allowed. Only mismatches are allowed.

I do know that this can be achieved using heavy penalty on insertion and deletion but was wondering if any dedicated algo exist.

As krobison has suggested, try NCBI's legacy bl2seq program to align 2 sequences to each other. I guess it's not available now. Try using the equivalent options in the newer blast+ suite.