Nematode.net v4.0



SiteMap	Home Sequencing Numbers Accession IDs Species List Library Details Data Download Software Staff Collaborators & Grants Publications FAQ NemaGene NemaBLAST NemaGene Search NemaBrowse Codon Usage Tables Function & Expression Putative Function - Kegg Putative Function - GO GO Associations Transcripts - Illumina RNA-Seq Transcripts - 454 cDNA Transcripts - Sanger ESTs Microarray Alternative Splicing sncRNAs Proteomics Comparative Genomics NemaPath Pathways ModDFS Modules InDels Cross-Tissue Compara gene families Helminth Control & Prevention HelmCoP Home Search for Gene Search for Ortholog HelmCoP BLAST HelmCoP FAQ Kinome Chokepoint Lysine Deacetylases Protein-protein interactions Microbiome Interaction MGS - Indonesia & Liberia 16s - Malaysia 16s - Australia 16s - Ecuador 16s - Indonesia 16s - Liberia Links NCBI WormBase WormBase Parasite NEMBASE4 Global NTD Research Sanger Institute 50 Helminth Genomes Project (50HGP) Helminth.net Washington University The Genome Institute

NemaGene : nemablast vs contigs

News

[Apr.22.2021]

New job listing! (click for details)

[Jan.24.2019]

Amazon awards research credit to support Helminth.net!

[July.10.2018]

Nematode.net is now hosted on Amazon!

Community Nematode.net user forum

Education Introduction to Nematodes Bioinformatics Workshop for Helminth Genomics Helminth.net Site Tutorial

FAQ Nematode.net FAQ NemaGene FAQ HelmCoP FAQ

Free-living Nematodes Caenorhabditis brenneri Caenorhabditis briggsae Caenorhabditis elegans Caenorhabditis japonica Caenorhabditis remanei Pristionchus pacificus Zeldia punctata

Human Parasitic Nematodes Ancylostoma ceylanicum Ancylostoma duodenale Ascaris lumbricoides Brugia malayi Loa loa Necator americanus Onchocerca volvulus Strongyloides stercoralis Trichinella spiralis Trichuris trichiura Wuchereria bancrofti

Plant Parasitic Nematodes Aphelenchoides besseyi Ditylenchus africanus Globodera pallida Globodera rostochiensis Heterodera glycines Heterodera schachtii Meloidogyne arenaria Meloidogyne artellia Meloidogyne chitwoodi Meloidogyne exigua Meloidogyne hapla Meloidogyne incognita Meloidogyne javanica Meloidogyne paranaensis Pratylenchus penetrans Pratylenchus vulnus Rodopholus similis Xiphinema index

Entomopathogenic Nematodes Heterorhabditis bacteriophora Steinernema carpocapsae

NemaBLAST versus transcript contigs, isotigs & genes:

Please enter your sequence here (must be in FASTA format)

Reset Entire Page

Select all the species you wish to include in your blast database by selecting individually or by clade from the menu below. Also be sure to enter your query sequence in the window above, either manually or fetch the sequence using the GenBank accession number. Next, choose the version of BLAST you want to run, and select whether or not to filter and mask your query. And be sure to enter your email address in the appropriate text box. Then finally press the BLAST Search button and your job will begin.

As of August 1st, 2011, NGS assembly contigs have been added into blast dbs where available. Typically these represent Newbler assemblies of 454 cDNA data. These references have been prefixed with a 4-letter abbreviation followed by an underscore to make them stand out from hits to older EST contigs (ex. Tcir_isotig00001).

As of November 1st, 2012, 10 CDS genesets are available as selectable dbs. These represent CDS for current, final set of genes from the organisms Ascaris suum, Brugia malayi, Bursaphelenchus xylophilus, Caenorhabditis elegans, Homo sapiens, Loa loa, Meloidogyne hapla, Schistosoma japonicum, Schistosoma mansoni and Trichinella spiralis. These CDS entries have been prefixed with the tag "CDS_<3|4-letter species code>|" (ex. CDS_Cele|...) to make them identifiable amongst other hits. The CDS fasta files being used as blast databases are available in our Data Download section at this link.

As of June 16th, 2017, 30 additional CDS genesets are available as selectable dbs. These represent CDS for a number of additional nematodes that have been added into NemaGene since the previous update. These CDS entries have been prefixed with the tag "CDS_<3|4-letter species code>" (ex. CDS_RSKR...) to make them identifiable amongst other hits, for an index of the prefixes assigned to specific organisms see the NemaGene FAQ. The CDS fasta files being used as blast databases have been made available at this link.

Select a BLAST type to use on this query:

Select from the following options:

Filtering:

Masking:

Please enter your email address
(for tracking your query, and emailing your BLAST output)

Must be in the form user@host.edu:

Use these buttons to select an entire clade at once






Use these buttons to select or deselect all databases

Press the BLAST Search button to execute your job (be sure to enter your email address in the appropriate box above)

Select NemaGene Database(s) to BLAST:

	Nematode.net v4.0(AWS) Copyright Statement
	User support forum Nematode.net User Support
Follow @nematodenet	Webmaster jmartin@wustl.edu