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

• Published in: Nucleic acids research Vol. 31; no. 13; pp. 3608 - 3612
• Main Authors: Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, Sbisà, Elisabetta, Pesole, Graziano
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-07-2003; Oxford Publishing Limited (England)
• Subjects: Base Sequence; Binding Sites; Consensus Sequence; DNA - chemistry; Internet; Nucleic Acid Conformation; Promoter Regions, Genetic; Regulatory Sequences, Nucleic Acid; Response Elements; RNA - chemistry; Sequence Analysis, DNA - methods; Sequence Analysis, RNA - methods; Software; Transcription Factors - metabolism; User-Computer Interface
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg548

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/.