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NemaBLAST versus transcript contigs, isotigs & genes:

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

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:

Clade I
geneset: Soboliphyme baturini
geneset: Trichinella nativa
Trichinella spiralis
geneset: Trichinella spiralis CDS
geneset: Trichuris trichiura
Trichuris vulpis
Trichuris muris
Xiphinema index

Clade III
geneset: Anisakis simplex
geneset: Ascaris lumbricoides
Ascaris suum
geneset: Ascaris suum CDS
Brugia malayi
Brugia malayi_Annotation
geneset: Brugia malayi CDS
geneset: Brugia pahangi
Dirofilaria immitis
geneset: Dracunculus medinensis
geneset: Elaeophora elaphi
geneset: Enterobius vermicularis
geneset: Gongylonema pulchrum
geneset: Loa loa CDS
Onchocerca flexuosa
geneset: Onchocerca ochengi
Onchocerca volvulus
geneset: Parascaris equorum
geneset: Syphacia muris
geneset: Thelazia callipaeda
Toxocara canis
geneset: Wuchereria bancrofti

Clade IVa
Parastrongyloides trichosuri
geneset: Rhabditophanes sp
geneset: Strongyloides papillosus
Strongyloides ratti
Strongyloides stercoralis
geneset: Strongyloides venezuelensis

Clade IVb
geneset: Bursaphelenchus xylophilus CDS
Ditylenchus africanus
Dictyocaulus viviparus
Globodera pallida
Globodera rostochiensis
Heterodera glycines
Heterodera schachtii
Laxus oneistus
Meloidogyne arenaria
Meloidogyne chitwoodi
Meloidogyne hapla
geneset: Meloidogyne hapla CDS
Meloidogyne incognita
Meloidogyne javanica
Meloidogyne paranaensis
Pratylenchus penetrans
Radopholus similis
Zeldia punctata

Clade V
Ancylostoma caninum
Ancylostoma caninum_Annotation_and_EST
Ancylostoma ceylanicum
geneset: Angiostrongylus cantonensis
geneset: Angiostrongylus costaricensis
geneset: Caenorhabditis angaria
geneset: Caenorhabditis brenneri
geneset: Caenorhabditis briggsae
Caenorhabditis elegans (wormpep nuc v190)
geneset: Caenorhabditis elegans CDS (WS230)
geneset: Caenorhabditis japonica
Caenorhabditis remanei
geneset: Caenorhabditis sp11
geneset: Caenorhabditis sp5
Cooperia oncophora
geneset: Cylicostephanus goldi
Haemonchus contortus
geneset: Haemonchus placei
geneset: Heligmosomoides polygyrus
Heterorhabditis bacteriophora
Necator americanus
Nippostrongylus brasiliensis
Oesophagostomum dentatum
Ostertagia ostertagi
Pristionchus pacificus
geneset: Strongylus vulgaris
Teladorsagia circumcincta
Trichostrongylus colubriformis

Outgroups
geneset: Homo sapiens CDS (GRCh37.66)


 
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