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

Nucleic Acids Res. 2003 Jul 1;31(13):3669-71. doi: 10.1093/nar/gkg596.

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/.

MeSH terms

  • Base Sequence
  • Codon
  • Internet
  • Markov Chains
  • Repetitive Sequences, Nucleic Acid*
  • Sequence Analysis, DNA / methods*
  • Software*
  • User-Computer Interface

Substances

  • Codon