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Literature DB >> 12824373

Regulatory sequence analysis tools.

Abstract

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.

Mesh：

Substances：
Transcription Factors

Year: 2003 PMID： 12824373 PMCID： PMC168973 DOI： 10.1093/nar/gkg567

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

9 in total

1. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.

Authors: H Salgado; A Santos-Zavaleta; S Gama-Castro; D Millán-Zárate; E Díaz-Peredo; F Sánchez-Solano; E Pérez-Rueda; C Bonavides-Martínez; J Collado-Vides
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

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Authors: G Z Hertz; G D Stormo
Journal: Bioinformatics Date: 1999 Jul-Aug Impact factor: 6.937

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Authors: J van Helden; A F Rios; J Collado-Vides
Journal: Nucleic Acids Res Date: 2000-04-15 Impact factor: 16.971

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Authors: J van Helden; B André; J Collado-Vides
Journal: Yeast Date: 2000-01-30 Impact factor: 3.239

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Journal: Comput Appl Biosci Date: 1990-04

6. Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

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Journal: Protein Sci Date: 1995-08 Impact factor: 6.725

7. SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

Authors: J Zhu; M Q Zhang
Journal: Bioinformatics Date: 1999 Jul-Aug Impact factor: 6.937

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Authors: J van Helden; B André; J Collado-Vides
Journal: J Mol Biol Date: 1998-09-04 Impact factor: 5.469

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

9 in total

219 in total

1. POBO, transcription factor binding site verification with bootstrapping.

Authors: Matti Kankainen; Liisa Holm
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

2. SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Authors: Zhenjun Hu; Yutao Fu; Anason S Halees; Szymon M Kielbasa; Zhiping Weng
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

3. Transcriptional analysis of the groES-groEL1, groEL2, and dnaK genes in Corynebacterium glutamicum: characterization of heat shock-induced promoters.

Authors: Carlos Barreiro; Eva González-Lavado; Miroslav Pátek; Juan-Francisco Martín
Journal: J Bacteriol Date: 2004-07 Impact factor: 3.490

4. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Authors: Morgane Thomas-Chollier; Andrew Hufton; Matthias Heinig; Sean O'Keeffe; Nassim El Masri; Helge G Roider; Thomas Manke; Martin Vingron
Journal: Nat Protoc Date: 2011-11-03 Impact factor: 13.491

5. Stb3 plays a role in the glucose-induced transition from quiescence to growth in Saccharomyces cerevisiae.

Authors: Dritan Liko; Michael K Conway; Douglas S Grunwald; Warren Heideman
Journal: Genetics Date: 2010-04-12 Impact factor: 4.562

6. Molecular control of polyene macrolide biosynthesis: direct binding of the regulator PimM to eight promoters of pimaricin genes and identification of binding boxes.

Authors: Javier Santos-Aberturas; Cláudia M Vicente; Susana M Guerra; Tamara D Payero; Juan F Martín; Jesús F Aparicio
Journal: J Biol Chem Date: 2010-12-27 Impact factor: 5.157

7. In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination.

Authors: Odil Porrua; Fruzsina Hobor; Jocelyne Boulay; Karel Kubicek; Yves D'Aubenton-Carafa; Rajani Kanth Gudipati; Richard Stefl; Domenico Libri
Journal: EMBO J Date: 2012-08-28 Impact factor: 11.598

8. AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.

Authors: Nils Ole Steffens; Claudia Galuschka; Martin Schindler; Lorenz Bülow; Reinhard Hehl
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

9. yMGV: a cross-species expression data mining tool.

Authors: Gaëlle Lelandais; Stéphane Le Crom; Frédéric Devaux; Stéphane Vialette; George M Church; Claude Jacq; Philippe Marc
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

10. The syp enhancer sequence plays a key role in transcriptional activation by the σ54-dependent response regulator SypG and in biofilm formation and host colonization by Vibrio fischeri.

Authors: Valerie A Ray; Justin L Eddy; Elizabeth A Hussa; Michael Misale; Karen L Visick
Journal: J Bacteriol Date: 2013-10-04 Impact factor: 3.490