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).