# gene prediction..?

**URL:** <https://community.alliancegenome.org/t/gene-prediction/4843>\
**Category:** WormBase\
**Created:** [February 17, 2014, 10:15pm UTC](https://community.alliancegenome.org/t/gene-prediction/4843 "2014-02-17T22:15:15Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Dolphin](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/d/779978/32.png) [@Dolphin](https://community.alliancegenome.org/u/Dolphin)\
**Post date:** [February 17, 2014, 10:15pm UTC](https://community.alliancegenome.org/t/gene-prediction/4843/1 "2014-02-17T22:15:15Z")

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

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**Author:** ![mh6](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/m/e495f1/32.png) [@mh6](https://community.alliancegenome.org/u/mh6)\
**Post date:** [February 18, 2014, 10:13am UTC](https://community.alliancegenome.org/t/gene-prediction/4843/2 "2014-02-18T10:13:16Z")

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

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**Author:** ![Dolphin](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/d/779978/32.png) [@Dolphin](https://community.alliancegenome.org/u/Dolphin)\
**Post date:** [February 18, 2014, 11:12am UTC](https://community.alliancegenome.org/t/gene-prediction/4843/3 "2014-02-18T11:12:24Z")

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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…

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**Author:** ![mh6](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/m/e495f1/32.png) [@mh6](https://community.alliancegenome.org/u/mh6)\
**Post date:** [February 18, 2014, 2:55pm UTC](https://community.alliancegenome.org/t/gene-prediction/4843/4 "2014-02-18T14:55:58Z")

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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](http://Nematode.net) and Nembase as good source for a large collection of parasitic nematode data (mostly transcripts, but some genomes as well).