Block-wise alignment of nucleotide sequences?

Kevin Karplus karplus at
Thu Mar 11 16:13:35 EST 2004

In article <us6f40lmlj468qrnsufpe65f307cqh0jql at>, Peter Frank wrote:
> I am looking for a program that allows me to perform block-wise
> alignment of nucleotide sequences (for example genomic and mRNA
> sequences). I tried out ClustalX but instead of finding blocks with
> perfect matching or high identity it gives me something completely
> else (long stretches with dispersed identical bases).
> Is there a program that performs block-wise alignment of nucleotide
> sequence pairs (i.e. I do not need multiple alignment here)? So far, I
> could only find programs capable of doing that with protein sequences.

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

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).

Kevin Karplus 	karplus at
life member (LAB, Adventure Cycling, American Youth Hostels)
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Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
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