Database tool GnpIS: an information system to integrate genetic and genomic data from plants and fungi

INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026, France*Corresponding author: Tel: +33 1 30 83 30 08; Fax: +33 1 30 83 38 99; Email: hadi.quesneville@versailles.inra.frSubmitted 5 March 2013; Revised 11 June 2013; Accepted 11 July 2013Citation details: Steinbach D, Alaux M, Amselem J, et al. GnpIS: an information system to integrate genetic and genomic data from plants andfungi. Database, Vol. 2013, Article ID bat058, doi:10.1093/database/bat058

[1]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[2]  P. Argos,et al.  SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.

[3]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[4]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[5]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[6]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[7]  Emmanuel Barillot,et al.  GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics , 2003, Nucleic Acids Res..

[8]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[9]  Manuel Ruiz,et al.  TropGENE-DB, a multi-tropical crop information system , 2004, Nucleic Acids Res..

[10]  Qunfeng Dong,et al.  MaizeGDB, the community database for maize genetics and genomics , 2004, Nucleic Acids Res..

[11]  Li Yang,et al.  MIPSPlantsDB—plant database resource for integrative and comparative plant genome research , 2007, Nucleic Acids Res..

[12]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[13]  Pierre Sourdille,et al.  A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B , 2008, Science.

[14]  Matthew D. Wilkerson,et al.  PlantGDB: a resource for comparative plant genomics , 2007, Nucleic Acids Res..

[15]  R. Drysdale FlyBase : a database for the Drosophila research community. , 2008, Methods in molecular biology.

[16]  Pierre Tufféry,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .

[17]  Liya Ren,et al.  Gramene QTL database: development, content and applications , 2009, Database J. Biol. Databases Curation.

[18]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[19]  Lincoln Stein,et al.  CMap 1.01: a comparative mapping application for the Internet , 2009, Bioinform..

[20]  J. Stajich,et al.  Using the Generic Synteny Browser (GBrowse_syn) , 2010, Current protocols in bioinformatics.

[21]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[22]  Jean,et al.  Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations , 2011, Nature communications.

[23]  Anton Nekrutenko,et al.  Integrating diverse databases into an unified analysis framework: a Galaxy approach , 2011, Database J. Biol. Databases Curation.

[24]  Junjun Zhang,et al.  BioMart: a data federation framework for large collaborative projects , 2011, Database J. Biol. Databases Curation.

[25]  Edward S. Buckler,et al.  Gramene database in 2010: updates and extensions , 2010, Nucleic Acids Res..

[26]  Michela Troggio,et al.  Genome sequence initiatives , 2011 .

[27]  Bernard Henrissat,et al.  Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea , 2011, PLoS genetics.

[28]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[29]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[30]  Jim Thurmond,et al.  FlyBase 101 – the basics of navigating FlyBase , 2011, Nucleic Acids Res..