Literature DB >> 12519948

ParaDB: a tool for paralogy mapping in vertebrate genomes.

Magalie Leveugle1, Karine Prat, Nadine Perrier, Daniel Birnbaum, François Coulier.   

Abstract

We present ParaDB (http://abi.marseille.inserm.fr/paradb/), a new database for large-scale paralogy studies in vertebrate genomes. We intended to collect all information (sequence, mapping and phylogenetic data) needed to map and detect new paralogous regions, previously defined as Paralogons. The AceDB database software was used to generate graphical objects and to organize data. General data were automatically collated from public sources (Ensembl, GadFly and RefSeq). ParaDB provides access to data derived from whole genome sequences (Homo sapiens, Mus musculus and Drosophila melanogaster): cDNA and protein sequences, positional information, bibliographical links. In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and 'In-Paralogs' data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data.

Entities:  

Mesh：

Substances：

Year:  2003        PMID： 12519948      PMCID： PMC165553          DOI： 10.1093/nar/gkg106

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


  21 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.  The probability of duplicate gene preservation by subfunctionalization.

Authors:  M Lynch; A Force
Journal:  Genetics       Date:  2000-01       Impact factor: 4.562

3.  Ancestrally-duplicated paraHOX gene clusters in humans.

Authors:  F Coulier; S Burtey; M Chaffanet; F Birg; D Birnbaum
Journal:  Int J Oncol       Date:  2000-09       Impact factor: 5.650

4.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

5.  Vertebrate evolution by interspecific hybridisation--are we polyploid?

Authors:  J Spring
Journal:  FEBS Lett       Date:  1997-01-02       Impact factor: 4.124

Review 6.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

7.  Duplication of large genomic regions during the evolution of vertebrate homeobox genes.

Authors:  K Schughart; C Kappen; F H Ruddle
Journal:  Proc Natl Acad Sci U S A       Date:  1989-09       Impact factor: 11.205

8.  Extensive genomic duplication during early chordate evolution.

Authors:  Aoife McLysaght; Karsten Hokamp; Kenneth H Wolfe
Journal:  Nat Genet       Date:  2002-05-28       Impact factor: 38.330

9.  Gene duplications and the origins of vertebrate development.

Authors:  P W Holland; J Garcia-Fernàndez; N A Williams; A Sidow
Journal:  Dev Suppl       Date:  1994

10.  The genome sequence of Drosophila melanogaster.

Authors:  M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728
View more
  5 in total

1.  TropGENE-DB, a multi-tropical crop information system.

Authors:  Manuel Ruiz; Mathieu Rouard; Louis Marie Raboin; Marc Lartaud; Pierre Lagoda; Brigitte Courtois
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species.

Authors:  Cédric Muller; Mathieu Denis; Laurent Gentzbittel; Thomas Faraut
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions.

Authors:  Magalie Leveugle; Karine Prat; Cornel Popovici; Daniel Birnbaum; François Coulier
Journal:  J Mol Evol       Date:  2004-02       Impact factor: 2.395

4.  SPODOBASE: an EST database for the lepidopteran crop pest Spodoptera.

Authors:  Vincent Nègre; Thierry Hôtelier; Anne-Nathalie Volkoff; Sylvie Gimenez; François Cousserans; Kazuei Mita; Xavier Sabau; Janick Rocher; Miguel López-Ferber; Emmanuelle d'Alençon; Pascaline Audant; Cécile Sabourault; Vincent Bidegainberry; Frédérique Hilliou; Philippe Fournier
Journal:  BMC Bioinformatics       Date:  2006-06-23       Impact factor: 3.169

5.  EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Authors:  Guohui Ding; Yan Sun; Hong Li; Zhen Wang; Haiwei Fan; Chuan Wang; Dan Yang; Yixue Li
Journal:  Nucleic Acids Res       Date:  2007-11-05       Impact factor: 16.971
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.