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