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Bioinformatics Vol. 19 no. 10 2003
Pages 1294-1295
© 2003 Oxford University Press

Applications Note

Longest biased interval and longest non-negative sum interval

Lloyd Allison

School of Computer Science and Software Engineering, Monash University, Clayton, Victoria, Australia 3800

Received on October 16, 2002 ; revised on November 17, 2002 ; accepted on January 22, 2003

Summary: Described is an algorithm to find the longest interval having at least a specified minimum bias in a sequence of characters (bases, amino acids), e.g. ‘at least 0.95 (A+T)-rich’. It is based on an algorithm to find the longest interval having a non-negative sum in a sequence of positive and negative numbers. In practice, it runs in linear time; this can be guaranteed if the bias is rational.

Availability: Java code of the algorithm can be found at http://www.csse.monash.edu.au/~lloyd/tildeProgLang/Java2/Biased/

Contact: lloyd{at}bruce.cs.monash.edu.au

Supplementary information: Examples of applications to Plasmodium falciparum genomic DNA can be found at the above URL.

* To whom correspondence should be addressed.


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