Gene finders

Here is a list of some gene-finders. This is only intended as a preliminary and incomplete list of gene-finders, and we hope very much that many other authors of gene-finders will participate in NGASP. Participation is open to all academic, private sector, and government researchers. We will be happy to add the name of your gene-finder to this list, when you contact us.*

Gene Prediction Software

• Acescan, Christopher Burge, website

• Aceview, Jean-Thierry Mieg - cDNA based; suitable for nGASP?

• Agene, Kasper Munch

• ASPic, Graziano Pesole -EST based; suitable for nGASP?

• Augustus, Mario Stanke - Avril

• CRAIG, Axel Bernal - Tristan

• Dogfish, David Carter, Richard Durbin - Avril

• EGPRED, G. Raghava

• Eugene, Eugene Team, Sylvain Foissac - Tristan

• Exogean, Hugues Roest Crollius

• Exonerate, Guy St C Slater, Ewan Birney - Avril

• ExonHunter, Tomas Vinar

• Fgenesh, Victor Solovyev or Softberry Inc. - Tristan

• Genefinder1 Wei-Min Chen ?- Avril

• Genefinder2 - LaDeana contacting Phil

• GeneID, GeneID team, Enrique Blanco, Roderic Guigo - Avril

• Genewise, Ewan Birney - Darin

• GeneZilla (evolved out of TigrScan), Bill Majoros - Tristan

• Genmark, Mark Borodovsky - Darin

• Genscan, Chris Burge - Avril

• GlimmerHMM Mihaela Pertea

• HMMGene, Anders Krogh - Avril

• mGene (previously named G3A) Gunnar Rätsch - Tristan

• Morgan (author notes that GlimmerM is major improvement), Steven Salzberg - Tristan

• SAGA , Lior Pachter

• SGP2, Roderic Guigo

• SNAP, Ian Korf - Avril

• SPIDA, Damian Keefe

• Twain, Bill Majoros - Tristan

• TIGRScan, Bill Majoros (Genezilla replaces TigrScan) - Tristan

• Twinscan, Michael Brent - Michael Brent to run

• UnVeil, Bill Majoros - Tristan

Combiners & Pipelines

• Avril's combiner - Avril

• DIGIT, Todd Taylor Yasushi Totoki (in Taylor's team)

• Ensembl Pipeline - Avril to ask Ensembl group

• GESECA combiner, Darin Blasiar - Gene Selection and Combining Algorithm

• Gramene evidence-based Pipeline (previously named Ensembl modified Pipeline), Chengzhi Liang - Tristan

• EuGene combiner, Thomas Schiex - Tristan

• Evigan, Qian Liu - Tristan

• GeneComber, Francis Ouellette

• GeneID - combiner mode, GeneID team, Enrique Blanco, Roderic Guigo

• GLEAN, Aaron Mackey - Avril

• Jigsaw, Jonathan Allen - Avril

• Vladimir Pavlovic's pipeline, Vladimir Pavlovic

*Disclaimer - Software and developers listed on the nGASP wiki do not necessarily endorse nor participate in the nGASP project but are listed solely for planning purposes.