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SIC: A tool to detect short inverted segments in a biological sequence.

TitleSIC: A tool to detect short inverted segments in a biological sequence.
Publication TypeJournal Article
Year of Publication2003
AuthorsRobelin, D, Richard, H, Prum, B
JournalNucleic Acids Res
Volume31
Issue13
Pagination3669-71
Date Published2003 Jul 1
ISSN1362-4962
KeywordsBase Sequence, Codon, Internet, Markov Chains, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Software, User-Computer Interface
Abstract

The web software SIC provides a tool to search for short inverted segments (length 3-5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of the scanning window and the order of the Markov chain. A list of the highest score segments is given with an assessment of the randomness of the result. SIC can be accessed via the URL: http://stat.genopole.cnrs.fr/SIC/.

Alternate JournalNucleic Acids Res.
PubMed ID12824390
PubMed Central IDPMC169195