The Seven State Aligner uses a dynamic programming algorithm to find the best alignment between two pieces of
DNA. This is designed for genomic to genomic comparisons, especially across species. Along with the alignment it
classifies areas as either coding (symbols 1,2,3), heavily conserved (symbol H), lightly conserved (symbol L) or
extended insert in either query or target (Q,T). The coding areas shouldn't be taken as gospel - this isn't a gene
finder, at least not yet.
Please limit the size of the top (query) sequence to less than 10,000 bases and the bottom (target) to less
than 100,000 bases. A 10,000 by 100,000 base alignment will take approximately 15 minutes. Two 1000 base alignments
will take approximately 15 seconds. The time is more dependent on the query length than target length once the
target is longer than 2000 bases..
Pattern to find (query):
DNA to search through (target):
Another WWW biological utility by Jim Kent.