Literature DB >> 12824415

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

Chenna Ramu1.   

Abstract

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Mesh：

Year:  2003        PMID： 12824415      PMCID： PMC168953          DOI： 10.1093/nar/gkg546

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


  16 in total

1.  RefSeq and LocusLink: NCBI gene-centered resources.

Authors:  K D Pruitt; D R Maglott
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  GCG: The Wisconsin Package of sequence analysis programs.

Authors:  D D Womble
Journal:  Methods Mol Biol       Date:  2000

3.  Object-oriented parsing of biological databases with Python.

Authors:  C Ramu; C Gemünd; T J Gibson
Journal:  Bioinformatics       Date:  2000-07       Impact factor: 6.937

Review 4.  Signature peptides. From analytical chemistry to functional genomics.

Authors:  H Karaoglu; I Humphery-Smith
Journal:  Methods Mol Biol       Date:  2000

5.  SIR: a simple indexing and retrieval system for biological flat file databases.

Authors:  C Ramu
Journal:  Bioinformatics       Date:  2001-08       Impact factor: 6.937

6.  The PROSITE database, its status in 2002.

Authors:  Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J A Sigrist; Kay Hofmann; Amos Bairoch
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  The Protein Information Resource: an integrated public resource of functional annotation of proteins.

Authors:  Cathy H Wu; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Robert S Ledley; Kali C Lewis; Hans-Werner Mewes; Bruce C Orcutt; Baris E Suzek; Akira Tsugita; C R Vinayaka; Lai-Su L Yeh; Jian Zhang; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

8.  The EMBL Nucleotide Sequence Database: major new developments.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

9.  Rapid and sensitive sequence comparison with FASTP and FASTA.

Authors:  W R Pearson
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

10.  SRS: information retrieval system for molecular biology data banks.

Authors:  T Etzold; A Ulyanov; P Argos
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600
View more
  10 in total

1.  ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.

Authors:  Pål Puntervoll; Rune Linding; Christine Gemünd; Sophie Chabanis-Davidson; Morten Mattingsdal; Scott Cameron; David M A Martin; Gabriele Ausiello; Barbara Brannetti; Anna Costantini; Fabrizio Ferrè; Vincenza Maselli; Allegra Via; Gianni Cesareni; Francesca Diella; Giulio Superti-Furga; Lucjan Wyrwicz; Chenna Ramu; Caroline McGuigan; Rambabu Gudavalli; Ivica Letunic; Peer Bork; Leszek Rychlewski; Bernhard Küster; Manuela Helmer-Citterich; William N Hunter; Rein Aasland; Toby J Gibson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

Authors:  Izabella Krystkowiak; Jean Manguy; Norman E Davey
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

3.  Mechanisms of zoonotic severe acute respiratory syndrome coronavirus host range expansion in human airway epithelium.

Authors:  Timothy Sheahan; Barry Rockx; Eric Donaldson; Amy Sims; Raymond Pickles; Davide Corti; Ralph Baric
Journal:  J Virol       Date:  2007-12-19       Impact factor: 5.103

4.  SLiMSearch 2.0: biological context for short linear motifs in proteins.

Authors:  Norman E Davey; Niall J Haslam; Denis C Shields; Richard J Edwards
Journal:  Nucleic Acids Res       Date:  2011-05-26       Impact factor: 16.971

5.  iELM--a web server to explore short linear motif-mediated interactions.

Authors:  Robert J Weatheritt; Peter Jehl; Holger Dinkel; Toby J Gibson
Journal:  Nucleic Acids Res       Date:  2012-05-25       Impact factor: 16.971

6.  DoReMi: context-based prioritization of linear motif matches.

Authors:  Heiko Horn; Niall Haslam; Lars Juhl Jensen
Journal:  PeerJ       Date:  2014-03-20       Impact factor: 2.984

7.  SeqNLS: nuclear localization signal prediction based on frequent pattern mining and linear motif scoring.

Authors:  Jhih-rong Lin; Jianjun Hu
Journal:  PLoS One       Date:  2013-10-29       Impact factor: 3.240

8.  SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.

Authors:  Izabella Krystkowiak; Norman E Davey
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

9.  ELM: the status of the 2010 eukaryotic linear motif resource.

Authors:  Cathryn M Gould; Francesca Diella; Allegra Via; Pål Puntervoll; Christine Gemünd; Sophie Chabanis-Davidson; Sushama Michael; Ahmed Sayadi; Jan Christian Bryne; Claudia Chica; Markus Seiler; Norman E Davey; Niall Haslam; Robert J Weatheritt; Aidan Budd; Tim Hughes; Jakub Pas; Leszek Rychlewski; Gilles Travé; Rein Aasland; Manuela Helmer-Citterich; Rune Linding; Toby J Gibson
Journal:  Nucleic Acids Res       Date:  2009-11-17       Impact factor: 16.971

10.  KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors.

Authors:  Francesca Diella; Sophie Chabanis; Katja Luck; Claudia Chica; Chenna Ramu; Claus Nerlov; Toby J Gibson
Journal:  Bioinformatics       Date:  2008-11-24       Impact factor: 6.937
  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.