title: PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.
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/.
authors.affiliation: Sezione di Bioinformatica e Genomica di Bari, Istituto Tecnologie Biomediche CNR, via Amendola 168/5, 70125 Bari, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Grillo
authors.forename: Flavio
authors.initials: F
authors.lastname: Licciulli
authors.forename: Sabino
authors.initials: S
authors.lastname: Liuni
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Sbisà
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry; D020407:Internet; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry; D012045:Regulatory Sequences, Nucleic Acid; D020218:Response Elements; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors; D012313:RNA; D004247:DNA