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


BACKGROUND
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.
Ramensky
V E
VE
Engelhardt Institute of Molecular Biology, Vavilova, 32 Moscow 117984, Russia. ramensky@imb.ac.ru
Makeev
V J
VJ
Roytberg
M A
MA
Tumanyan
V G
VG
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D016678:Genome; D023281:Genomics / Q000706:statistics & numerical data; D010963:Plasmodium falciparum / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software