PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences

Nucleic Acids Res. 2003 Jul 1;31(13):3608-12. doi: 10.1093/nar/gkg548.

Abstract

Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection of such cis-acting elements in genome-wide screenings may significantly contribute to genome annotation and comparative analysis as well as to target functional characterization experiments. We present here PatSearch, a flexible and fast pattern matcher able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices. It can also allow for mismatches/mispairings below a user fixed threshold. We report three different applications of the program in the search of complex patterns such as those of the iron responsive element hairpin-loop structure, the p53 responsive element and a promoter module containing CAAT-, TATA- and cap-boxes. PatSearch is available on the web at http://bighost.area.ba.cnr.it/BIG/PatSearch/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Consensus Sequence
  • DNA / chemistry
  • Internet
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • RNA / chemistry
  • Regulatory Sequences, Nucleic Acid*
  • Response Elements
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, RNA / methods*
  • Software*
  • Transcription Factors / metabolism
  • User-Computer Interface

Substances

  • Transcription Factors
  • RNA
  • DNA