Literature DB >> 12824377

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

Giorgio Grillo1, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Graziano Pesole.   

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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Year:  2003        PMID： 12824377      PMCID： PMC168955          DOI： 10.1093/nar/gkg548

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  16 in total

Review 1.  Discovery and modeling of transcriptional regulatory regions.

Authors:  J W Fickett; W W Wasserman
Journal:  Curr Opin Biotechnol       Date:  2000-02       Impact factor: 9.740

2.  Computer-assisted analysis of transcription control regions. Matinspector and other programs.

Authors:  T Werner
Journal:  Methods Mol Biol       Date:  2000

3.  PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.

Authors:  G Pesole; S Liuni; M D'Souza
Journal:  Bioinformatics       Date:  2000-05       Impact factor: 6.937

4.  The Eukaryotic Promoter Database (EPD): recent developments.

Authors:  R C Périer; T Junier; C Bonnard; P Bucher
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

5.  Further characterisation of the p53 responsive element--identification of new candidate genes for trans-activation by p53.

Authors:  J C Bourdon; V Deguin-Chambon; J C Lelong; P Dessen; P May; B Debuire; E May
Journal:  Oncogene       Date:  1997-01-09       Impact factor: 9.867

6.  Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.

Authors:  P Bucher
Journal:  J Mol Biol       Date:  1990-04-20       Impact factor: 5.469

Review 7.  Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress.

Authors:  M W Hentze; L C Kühn
Journal:  Proc Natl Acad Sci U S A       Date:  1996-08-06       Impact factor: 11.205

8.  The sequence of the stem and flanking sequences at the 3' end of histone mRNA are critical determinants for the binding of the stem-loop binding protein.

Authors:  A S Williams; W F Marzluff
Journal:  Nucleic Acids Res       Date:  1995-02-25       Impact factor: 16.971

9.  TRANSFAC: transcriptional regulation, from patterns to profiles.

Authors:  V Matys; E Fricke; R Geffers; E Gössling; M Haubrock; R Hehl; K Hornischer; D Karas; A E Kel; O V Kel-Margoulis; D-U Kloos; S Land; B Lewicki-Potapov; H Michael; R Münch; I Reuter; S Rotert; H Saxel; M Scheer; S Thiele; E Wingender
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 10.  The p53/p63/p73 family of transcription factors: overlapping and distinct functions.

Authors:  M Levrero; V De Laurenzi; A Costanzo; J Gong; J Y Wang; G Melino
Journal:  J Cell Sci       Date:  2000-05       Impact factor: 5.285
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  52 in total

Review 1.  Searching for IRES.

Authors:  Stephen D Baird; Marcel Turcotte; Robert G Korneluk; Martin Holcik
Journal:  RNA       Date:  2006-09-06       Impact factor: 4.942

2.  DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression.

Authors:  Rupak Mukhopadhyay; Partho Sarothi Ray; Abul Arif; Anna K Brady; Michael Kinter; Paul L Fox
Journal:  Mol Cell       Date:  2008-11-07       Impact factor: 17.970

3.  Contributions of specificity protein-1 and steroidogenic factor 1 to Adcy4 expression in Y1 mouse adrenal cells.

Authors:  Xianliang Rui; Jennivine Tsao; Joshua O Scheys; Gary D Hammer; Bernard P Schimmer
Journal:  Endocrinology       Date:  2008-04-03       Impact factor: 4.736

4.  Box H/ACA snoRNAs are preferred substrates for the trimethylguanosine synthase in the divergent unicellular eukaryote Trichomonas vaginalis.

Authors:  Augusto Simoes-Barbosa; Kausik Chakrabarti; Michael Pearson; Delphine Benarroch; Stewart Shuman; Patricia J Johnson
Journal:  RNA       Date:  2012-07-30       Impact factor: 4.942

5.  TGF-beta-mediated phosphorylation of hnRNP E1 induces EMT via transcript-selective translational induction of Dab2 and ILEI.

Authors:  Arindam Chaudhury; George S Hussey; Partho S Ray; Ge Jin; Paul L Fox; Philip H Howe
Journal:  Nat Cell Biol       Date:  2010-02-14       Impact factor: 28.824

6.  Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts.

Authors:  Yoshinori Hatakeyama; Norihiro Shibuya; Takashi Nishiyama; Nobuhiko Nakashima
Journal:  RNA       Date:  2004-05       Impact factor: 4.942

Review 7.  The GAIT system: a gatekeeper of inflammatory gene expression.

Authors:  Rupak Mukhopadhyay; Jie Jia; Abul Arif; Partho Sarothi Ray; Paul L Fox
Journal:  Trends Biochem Sci       Date:  2009-06-15       Impact factor: 13.807

8.  Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures.

Authors:  You Li; Eric S Ho; Samuel I Gunderson; Megerditch Kiledjian
Journal:  Nucleic Acids Res       Date:  2009-02-20       Impact factor: 16.971

9.  Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences.

Authors:  Marie Brázdová; Timo Quante; Lars Tögel; Korden Walter; Christine Loscher; Vlastimil Tichý; Lenka Cincárová; Wolfgang Deppert; Genrich V Tolstonog
Journal:  Nucleic Acids Res       Date:  2009-01-12       Impact factor: 16.971

10.  UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Authors:  Giorgio Grillo; Antonio Turi; Flavio Licciulli; Flavio Mignone; Sabino Liuni; Sandro Banfi; Vincenzo Alessandro Gennarino; David S Horner; Giulio Pavesi; Ernesto Picardi; Graziano Pesole
Journal:  Nucleic Acids Res       Date:  2009-10-30       Impact factor: 16.971
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