Literature DB >> 14681448

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes.

Todd Wylie1, John C Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W Clifton, Asif Chinwalla, Robert H Waterston, Richard K Wilson, James P McCarter.   

Abstract

Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. A sister project at the University of Edinburgh and the Sanger Institute is also underway. More than 295,000 ESTs have been generated from >30 nematodes other than Caenorhabditis elegans including key parasites of humans, animals and plants. Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the ongoing generation of nematode genome data. The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species.

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Year:  2004        PMID： 14681448      PMCID： PMC308745          DOI： 10.1093/nar/gkh010

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


  17 in total

Review 1.  The KEGG database.

Authors:  Minoru Kanehisa
Journal:  Novartis Found Symp       Date:  2002

2.  The InterPro Database, 2003 brings increased coverage and new features.

Authors:  Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard R Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Sam Griffiths-Jones; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; David Lonsdale; Ville Silventoinen; Sandra E Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Jeremy D Selengut; Florence Servant; Christian J A Sigrist; Robert Vaughan; Evgueni M Zdobnov
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  400000 nematode ESTs on the Net.

Authors:  John Parkinson; Makedonka Mitreva; Neil Hall; Mark Blaxter; James P McCarter
Journal:  Trends Parasitol       Date:  2003-07

4.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

5.  The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi.

Authors:  S A Williams; M R Lizotte-Waniewski; J Foster; D Guiliano; J Daub; A L Scott; B Slatko; M L Blaxter
Journal:  Int J Parasitol       Date:  2000-04-10       Impact factor: 3.981

Review 6.  The genomes of Onchocerca volvulus.

Authors:  T R Unnasch; S A Williams
Journal:  Int J Parasitol       Date:  2000-04-10       Impact factor: 3.981

7.  A molecular evolutionary framework for the phylum Nematoda.

Authors:  M L Blaxter; P De Ley; J R Garey; L X Liu; P Scheldeman; A Vierstraete; J R Vanfleteren; L Y Mackey; M Dorris; L M Frisse; J T Vida; W K Thomas
Journal:  Nature       Date:  1998-03-05       Impact factor: 49.962

Review 8.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

9.  WormBase: a cross-species database for comparative genomics.

Authors:  Todd W Harris; Raymond Lee; Erich Schwarz; Keith Bradnam; Daniel Lawson; Wen Chen; Darin Blasier; Eimear Kenny; Fiona Cunningham; Ranjana Kishore; Juancarlos Chan; Hans-Michael Muller; Andrei Petcherski; Gudmundur Thorisson; Allen Day; Tamberlyn Bieri; Anthony Rogers; Chao-Kung Chen; John Spieth; Paul Sternberg; Richard Durbin; Lincoln D Stein
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  The distributed annotation system.

Authors:  R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal:  BMC Bioinformatics       Date:  2001-10-10       Impact factor: 3.169
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  35 in total

1.  The role of pseudo-endoglucanases in the evolution of nematode cell wall-modifying proteins.

Authors:  Annelies Haegeman; Tina Kyndt; Godelieve Gheysen
Journal:  J Mol Evol       Date:  2010-04-23       Impact factor: 2.395

2.  Expression profile of heat shock response factors during hookworm larval activation and parasitic development.

Authors:  Verena Gelmedin; Angela Delaney; Lucas Jennelle; John M Hawdon
Journal:  Mol Biochem Parasitol       Date:  2015-08-18       Impact factor: 1.759

3.  Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii.

Authors:  Bartel Vanholme; Makedonka Mitreva; Wim Van Criekinge; Marc Logghe; David Bird; James P McCarter; Godelieve Gheysen
Journal:  Parasitol Res       Date:  2005-12-28       Impact factor: 2.289

4.  A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.

Authors:  M Mitreva; A A Elling; M Dante; A P Kloek; A Kalyanaraman; S Aluru; S W Clifton; D McK Bird; T J Baum; J P McCarter
Journal:  Mol Genet Genomics       Date:  2004-08-28       Impact factor: 3.291

5.  Exploring the transcriptome of the burrowing nematode Radopholus similis.

Authors:  Joachim Jacob; Makedonka Mitreva; Bartel Vanholme; Godelieve Gheysen
Journal:  Mol Genet Genomics       Date:  2008-04-02       Impact factor: 3.291

6.  Transcripts analysis of the entomopathogenic nematode Steinernema carpocapsae induced in vitro with insect haemolymph.

Authors:  You-Jin Hao; Rafael Montiel; Sahar Abubucker; Makedonka Mitreva; Nelson Simões
Journal:  Mol Biochem Parasitol       Date:  2009-10-27       Impact factor: 1.759

Review 7.  The biology and genomics of Strongyloides.

Authors:  M E Viney
Journal:  Med Microbiol Immunol       Date:  2006-03-15       Impact factor: 3.402

8.  Oscheius tipulae as an example of eEF1A gene diversity in nematodes.

Authors:  Rubens N Akamine; Carlos Eduardo Winter
Journal:  J Mol Evol       Date:  2008-08-12       Impact factor: 2.395

9.  Structural and functional characterization of a secreted hookworm Macrophage Migration Inhibitory Factor (MIF) that interacts with the human MIF receptor CD74.

Authors:  Yoonsang Cho; Brian F Jones; Jon J Vermeire; Lin Leng; Lisa DiFedele; Lisa M Harrison; Huabao Xiong; Yuen-Kwan Amy Kwong; Yibang Chen; Richard Bucala; Elias Lolis; Michael Cappello
Journal:  J Biol Chem       Date:  2007-06-13       Impact factor: 5.157

10.  Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics.

Authors:  John Martin; Sahar Abubucker; Todd Wylie; Yong Yin; Zhengyuan Wang; Makedonka Mitreva
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971
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