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Protocols

Nematode.net specifications

Information


Unique identifier OMICS_02754
Name Nematode.net
Restrictions to use None
Database management system MySQL
Community driven Yes
User data submission Not allowed
Version 4.0
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans

Subtools


  • NemaBlast
  • NemaBrowse
  • NemaGene
  • NemaPath

Documentation


Maintainers


  • person_outline Makedonka Mitreva
  • person_outline John Martin

Publications for Nematode.net

Nematode.net citations

 (28)
library_books

The Distribution of Lectins across the Phylum Nematoda: A Genome Wide Search

2017
Int J Mol Sci
PMCID: 5297725
PMID: 28054982
DOI: 10.3390/ijms18010091

[…] n addition, transcriptome databases of some plant parasitic nematodes were searched for lectin-like domains as well: Hirschmanniella oryzae [], Meloidogyne graminicola [], Heterodera glycines (http://nematode.net), Heterodera avenae [], Pratylenchus coffeae [], and Pratylenchus thornei []. All new hits were checked separately to reduce the number of false positives. The nematode-specific profile w […]

library_books

The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates

2016
PMCID: 5039805
PMID: 27677574
DOI: 10.1186/s13071-016-1795-8

[…] sources (golden hamster genome database, GCF_000349665.1, and GenBank Bacterial Sequences database, GBBCT). The processed reads were mapped to the unpublished A. ceylanicum genome (available at http: nematode.net []), using Tophat 2.0.8 [] with the parameter mate-inner-distance set to 300. Breadth of coverage and read count of individual A. ceylanicum gene transcripts were calculated using Refcov, […]

library_books

Paramyosin of canine Onchocerca lupi: usefulness for the diagnosis of a neglected zoonotic disease

2016
PMCID: 5013582
PMID: 27604904
DOI: 10.1186/s13071-016-1783-z

[…] s from other organisms were identified by BLASTp of non-redundant (NCBI, www.pantherdb.org/, www.metazoa.ensembl.org) and parasite-specific databases (www.broadinstitute.org/, www.nematodes.org/, www.nematode.net/, www.wormbase.org). Augustus gene prediction, using B. malayi as the training set, was used to predict the full-length genes and proteins from genomic data (http://bioinf.uni-greifswald. […]

library_books

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

2016
BMC Evol Biol
PMCID: 4828791
PMID: 27068610
DOI: 10.1186/s12862-016-0651-y

[…] []. We performed searches against all available nematode clades as well as to Hoplolaimina PPN separately. As outgroups in these searches, we included the genesets from flatworms and Homo sapiens at Nematode.net, but as our main outgroup, we included the genomic sequences for the Tardigrade Hypsibius dujardini []; Tardigrada (water bears) is another basal Ecdysozoa phylum like Nematoda. Also, we […]

library_books

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention

2016
Sci Rep
PMCID: 4746573
PMID: 26856411
DOI: 10.1038/srep20316

[…] re predicted using DESeq2 (version 1.4.5) with an adjusted p-value cutoff of 0.1 according to established protocols. Statistical enrichments are described in . RNA-Seq profiles have been deposited in Nematode.net and a browse-able genome is also available at Nematode.net and WormBase. […]

call_split

Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root Knot Nematode Meloidogyne incognita

2015
PLoS One
PMCID: 4339843
PMID: 25710378
DOI: 10.1371/journal.pone.0118269
call_split See protocol

[…] notated and assigned to known functional groups as previously described []. For detection of differentially expressed transcripts in nematodes a publicly available M. incognita database was used (www.nematode.net). […]

Citations

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Nematode.net institution(s)
The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Microbiology, Immunology & Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA; Department of Internal Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
Nematode.net funding source(s)
Supported by National Institutes of Health (NIH) [AI081803 and GM097435]; NIFA [2013-01109]; OPP [GH 1083853], NIH-NHGRI [U54HG003079], and NIH [AI098639, CA164719 and CA155297].

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