gene prediction..?

Model Organism: Worms WormBase
1

I know of Augustus and mGene but are there any other gene prediction programs that focus on nematode sequences?

2

We ran that competition a while ago: http://wiki.wormbase.org/index.php/NGASP
(the paper is here: http://www.biomedcentral.com/1471-2105/9/549)

All participating groups customised their prediction pipelines specifically for the competition, so they should have at the very least optimised C.elegans settings.
In addition we have a cooperation with a group that uses Maker to predict genes on parasitic nematodes, which seems to work also quite well.

3

Thanks - I’ve looked at Maker and the possibility to include a ‘guide’ protein sequence looks useful.
I’m collecting unannotated unfinished sequences from various parasitic genomes and then putting together a conserved protein sequence present in each.
I am, however, finding navigation between the various parasitic nematode genome sites rather confusing…

4

WormBase just started a spin-off project to collect and present parasitic nematode data in an uniform way, but it just started.

I can also recommend Nematode.net and Nembase as good source for a large collection of parasitic nematode data (mostly transcripts, but some genomes as well).