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

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

Giorgio Grillo  1 , Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Graziano Pesole
Affiliations

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

Giorgio Grillo et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1
Figure 1
The consensus structures of the iron responsive elements (IRE) (A); the relevant PatSearch pattern syntax (B); part of PatSearch output obtained on a set of 5′ UTRs collected in UTRdb (C).
Figure 2
Figure 2
PatSearch syntax for the p53 responsive element including two post-processing steps and a constraint on the total length of decamer spacers (A); partial output obtained searching the pattern in the EPD database (13) (B).
Figure 3
Figure 3
(A) PatSearch syntax for a promoter module made of a CAAT-box, a TATA-box and a cap-box (TRANSFAC IDs V$CAAT_01, V$TATA_01, V$CAP_01). The * denotes core promoter positions to which an higher similarity cutoff is assigned; (B) partial output obtained searching the pattern in human EPD sequences (13).
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