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

Grillo Giorgio, Giorgio and Licciulli, Flavio and Liuni, Sabino and Sbisà, Elisabetta and Pesole, Graziano (2003) PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Research, 31 (13). pp. 3608-3612. ISSN 1362-4962

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Official URL: http://nar.oxfordjournals.org/content/31/13/3608.s...

Abstract

Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corre- sponding trans-acting protein factors. Detection of such cis-acting elements in genome-wide screen- ings may significantly contribute to genome annota- tion 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 oligonu- cleotide 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 applica- tions 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/.

Item Type: Article
Subjects: 500 Scienze naturali e Matematica > 570 Scienze della vita; Biologia
Depositing User: Sabino SL Liuni
Date Deposited: 21 Dec 2016 13:31
Last Modified: 21 Dec 2016 13:31
URI: http://eprints.bice.rm.cnr.it/id/eprint/15450

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