Block-wise alignment of nucleotide sequences?

[Peter Frank]

Kevin Karplus wrote:

>Clustal is a global aligner and nearly useless for local alignment.
>You may just need a local aligner rather than a global one.

That is what I assumed.

>Try BLAST or BLAT, both do a pretty good job of aligning mRNA and
>genomic sequences (even EST and genomic, though that's a bit harder,
>because of the sequencing noise in EST sequences).

Thanks for the advice. I will try these. So far I have only used BLAST
for doing database seaches.

Peter