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Bioinformatics Vol. 17 no. 11 2001
Pages 1065-1066
© 2001 Oxford University Press

Applications Note

Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software

Vasily E. Ramensky 1,*, Vsevolod Ju. Makeev 1, Mikhail A. Roytberg 2 and Vladimir G. Tumanyan 1

1 Engelhardt Institute of Molecular Biology, Vavilova, 32 Moscow 117984, Russia
2 Institute of Mathematical Problems of Biology, Institutskaya, 4 Puschino, Moscow region 142292, Russia

Received on December 13, 2000 ; revised on May 29, 2001 ; accepted on June 4, 2001

Summary: We present a software system BASIO that allows one to segment a sequence into regions with homogeneous nucleotide composition at a desired length scale. The system can work with arbitrary alphabet and therefore can be applied to various (e.g. protein) sequences. Several sequences of complete genomes of eukaryotes are used to demonstrate the efficiency of the software.

Availability: The BASIO suite is available for non-commercial users free of charge as a set of executables and accompanying segmentation scenarios from http://www.imb.ac.ru/compbio/basio. To obtain the source code, contact the authors.

Contact: basio{at}imb.ac.ru; ramensky{at}imb.ac.ru; makeev{at}imb.ac.ru

* To whom correspondence should be addressed.


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