Bioinformatics Vol. 17 no. 90001 2001
Pages S207-S214
© 2001 Oxford University Press
An algorithm for finding signals of unknown length in DNA sequences
1 Department of Computer Science, Systems
and Communication, University of Milan–Bicocca, Via Bicocca
degli Arcimboldi 8, Milan, I-20126, Italy
2 Department of General Physiology and
Biochemistry, University of Milan, Via Celoria 20, Milan, I-20133,
Italy
Received on February 5, 2001
; revised on April 3, 2001
; accepted on April 3, 2001
Pattern discovery in unaligned DNA sequences is a
challenging problem in both computer science and molecular biology.
Several different methods and techniques have been proposed so far,
but in most of the cases signals in DNA sequences are very
complicated and avoid detection. Exact exhaustive methods can solve
the problem only for short signals with a limited number of
mutations. In this work, we extend exhaustive enumeration also to
longer patterns. More in detail, the basic version of algorithm
presented in this paper, given as input a set of sequences and an
error ratio 
< 1, finds all patterns that occur in at
least q sequences of the set with at most
m mutations, where m is the length of the pattern.
The only restriction is imposed on the location of mutations along
the signal. That is, a valid occurrence of a pattern can present at
most 
i
mismatches in the first
i nucleotides, and so on. However, we show how the algorithm
can be used also when no assumption can be made on the position of
mutations. In this case, it is also possible to have an estimate of
the probability of finding a signal according to the signal length,
the error ratio, and the input parameters. Finally, we discuss some
significance measures that can be used to sort the patterns output by
the algorithm.
Contact: pavesi{at}disco.unimib.it
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