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NemaGene Clustering - Search our collection of transcript clusters


Instructions specific to this page

NemaGene can be searched by stage, isogroup/cluster name, gene/isotig/contig name or cDNA read name on a per species basis. Enter your search term in the box labeled Enter search below:. Then select the appropriate settings from the Search Type: and Species Database: dropboxes. Be aware that if you do not set these dropbox menus your selection will most likely not be found. Click on the Search Clusters button to begin your search. All isotigs/contigs for the selected species of your requested type will be displayed. Some searches that return long lists of isotigs/contigs may take a long time to display.

For more information on NemaGene please see our NemaGene FAQ.

How to use this page

Most access into the NemaGene database comes from other tools within the Nematode.net site such as the contig links from NemaPath which directly jump to the contig details pages that are the terminus of a NemaGene search. But the NemaGene cluster search form can also be of use when you have identified a contig, isotig or gene from some other Nematode.net resources (eg. a pan-phylum NemaBLAST result or a cluster of interest from our FTP service) and want more detail on that sequence entity. Another common use would be identifying a stage specific set of isotigs/contigs for a given organism using the 'Stage' search selection.

NemaGene Geneset summary tables

The Geneset table towards the bottom of this page provides details on the numbers and data source of finished genesets available in NemaGene. It shows the number of gene isoforms and gene loci if that information is available, in cases where locus-isoform information is not known, genes are all stored as unique isoforms. The data source version is also displayed, as well as an example of a typical gene name for that organism.

NemaGene Transcript summary tables

The tables at the bottom of this page detail the numbers of clusters/isogroups, contigs/isotigs, and cDNA reads used in the transcript assembly of each listed species divided by sequencing platform. It also displays the # of Sanger cDNA reads for each organism present in dbEST as of the listed date to give visitors an idea of how complete a given Sanger-based transcript assembly is compared to currently available data.

Data archive

In the case of an older transcript assembly being replaced with a newer assembly, the old data can be downloaded from the Data FTP page (in the "Older Clustering Files" section).


Search Examples:
Stage: Search for all isotigs/contigs containing reads of a given life cycle stage for the chosen species (other stages may also be present, but every reported isotig or contig is gauranteed to comprise at least one read from the chosen stage). L2

L3

Female

note: choosing the stage 'Adult' will return both adult male and female containing isotigs/contigs
NemaGene Isotig/contig ID: Search by NemaGene isotig or contig name. (isotig name from RNAseq Ancylostoma caninum) Acan_isotig12281

(contig name from Ancylostoma ceylanicum) AE00100
NemaGene isogroup/cluster ID: Search by NemaGene isogroup or cluster name. (isogroup name from RNAseq Ancylostoma caninum) Acan_isogroup08334

(cluster name from Ancylostoma ceylanicum) AE00072.cl
cDNA read name:
Enter NemaGene name for a cDNA read from the selected species. The result will display the isotig or contig in which the cDNA read is a member. (old sanger read from Ancylostoma ceylanicum) pk07b07.x1

(454 read from RNAseq A.caninum) EXWOO7002IL5TE
Gene Locus: Search by gene locus name. (...example pending...)
Gene: Search by gene (isoform) name. (Brugia malayi gene name from WS230) BM09831
Search Type:
Species Database:
Enter search below:
Genesets (last updated: 10/17/12)
Active Genes
# Gene Isoforms
# Gene Loci
Data source
Example Gene name
Brugia malayi
21,332
na
WS230
BM09831
454-based transcripts (last updated: 9/15/11)
Active NemaGene Clusters
# Isogroups/Clusters
# Genes/Isotigs/Contigs
# 454 cDNAs
ID Prefix
Ancylostoma caninum
19,277
29,448
1,483,002
Acan
Cooperia oncophora
19,955
31,302
1,319,363
Conc
Dictyocaulus viviparus
20,571
36,192
1,330,579
Dviv
Heterorhabditis bacteriophora
7,320
7,320
580,165
Hbac
Necator americanus
9,262
9,692
507,397
Name
Oesophagostomum dentatum
16,885
29,805
1,268,664
Oden
Ostertagia ostertagi
16,416
29,939
1,596,628
Oost
Teladorsagia circumcincta
30,118
33,101
885,913
Tcir
Trichostrongylus colubriformis
20,214
27,412
2,399,700
Tcol
Sanger-based transcripts (last updated: 10/26/11)
Active NemaGene Clusters
# Clusters
# Genes/Contigs
# Sanger cDNAs
# dbEST
ID Prefix
Ancylostoma ceylanicum
3,369
4,953
10,588
10,651
AE
Ascaris suum
9,949
17,989
39,162
56,616
AS
Brugia malayi
1,310
1,609
3,742
26,215
BM
Caenorhabditis remanei
9,560
12,334
21,503
20,292
CR
Dirofilaria immitis
1,793
2,534
3,999
4,005
DI
Ditylenchus africanus
3,808
5,214
6,528
4,847
DA
Globodera pallida
2,257
2,973
4,389
9,020
GP
Globodera rostochiensis
6,448
9,482
15,687
11,851
GR
Haemonchus contortus
5,058
9,842
22,152
21,975
HC
Heterodera schachtii
1,555
1,600
2,849
2,812
HS
Heterodera glycines
8,638
12,313
24,366
24,444
HG
Meloidogyne arenaria
3,241
3,372
5,019
5,042
MA
Meloidogyne chitwoodi
3,578
5,880
12,187
12,218
MC
Meloidogyne hapla
6,667
11,193
24,331
24,452
MH
Meloidogyne incognita
5,598
9,107
19,957
20,334
MI
Meloidogyne javanica
4,827
5,172
7,594
7,587
MJ
Meloidogyne paranaensis
2,156
2,263
3,710
3,710
MP
Nippostrongylus brasiliensis
2,997
4,532
14,686
14,686
NB
Onchocerca flexuosa
1,476
1,665
2,124
2,124
OF
Ostertagia ostertagi (archived old version)
2,313
4,659
7,020
7,006
OS
Parastrongyloides trichosuri
4,324
4,934
7,914
7,963
PT
Pratylenchus penetrans
420
488
1,928
1,916
PE
Pristionchus pacificus
2,603
2,654
4,979
37,470
PP
Radopholus similis
4,004
5,551
6,982
7,382
RS
Steinernema carpocapsae
1,387
1,592
2,015
2,218
SC
Strongyloides ratti
4,152
5,237
14,703
27,366
SR
Strongyloides stercoralis
3,311
3,479
10,908
11,392
SS
Toxocara canis
1,975
2,135
4,902
5,069
TX
Trichinella spiralis
3,453
5,958
10,130
25,268
TS
Trichuris muris
2,650
3,735
7,170
7,102
TM
Trichuris vulpis
1,224
1,690
3,062
3,063
TV
Xiphinema index
5,400
5,485
9,344
9,351
XI
Zeldia punctata
195
202
378
391
ZP



 
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