Block-wise alignment of nucleotide sequences?

Peter Frank peter_frankde at
Mon Mar 8 13:03:47 EST 2004


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.


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