PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences (Articolo in rivista)

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Label
  • PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences (Articolo in rivista) (literal)
Anno
  • 2003-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1093/nar/gkg548 (literal)
Alternative label
  • Grillo G., Licciulli F., Liuni S., Sbisà E., Pesole G. (2003)
    PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
    in Nucleic acids research
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Grillo G., Licciulli F., Liuni S., Sbisà E., Pesole G. (literal)
Pagina inizio
  • 1 (literal)
Pagina fine
  • 5 (literal)
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  • 31 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 13 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#descrizioneSinteticaDelProdotto
  • 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. (literal)
Note
  • ISI Web of Science (WOS) (literal)
  • SCImago (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Istituto di Tecnologie Biomediche - Sezione di Bari Università di Milano (literal)
Titolo
  • PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences (literal)
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://www.ba.itb.cnr.it/BIG/PatSearch/. (literal)
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