PALINDROME

Looks for inverted repeats in a nucleotide sequence

palindrome looks for inverted repeats (stem loops) in anucleotide sequence.

It will find inverted repeats that include a proportion of mismatchesand gaps (bulges in the stem loop).

It works by finding all possible inverted matches satisfying thespecified conditions of minimum and maximum length of palindrome,maximum gap between repeated regions and number of mismatches allowed.

Secondary structures like inverted repeats in genomic sequences may beimplicated in initiation of DNA replication.

Some genomic sequence entries in the databases are composed ofunfinished, draft sequence with gaps of unknown size between contigs. The positions of these gaps are often indicated by runs of 200 Ncharacters. To prevent palindrome producing large, uninformativeoutputs, any palindromes found that are composed only of N's will not bereported.

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