Gene prediction

Gene prediction tools

Support for gene prediction tools are listed here. The Run package also lists the current wrapper modules for running gene prediction tools.

If you have additional tools that are requested, please add them to the list with a mention of WANTED.

Modules to parse Gene prediction results

The modules are named with the same name as the prediction program so hopefully it is clear. In addition variants are supported where possible (Fgenesh++ should be parseable with Fgenesh, GlimerHMM with Glimmer, etc).

Ab initio

• Bio::Tools::Geneid
• Bio::Tools::Genemark (WANTED - verify the prokaryotic formats parse, eg. GeneMarkS)
• Bio::Tools::Genscan
• Bio::Tools::Glimmer
• Bio::Tools::Grail
• Bio::Tools::Fgenesh
• Bio::Tools::MZEF
• Bio::Tools::tRNAscanSE - tRNA genes
• Bio::Tools::rfamscan (WANTED - rfamscan, a tool which uses Infernal and rfam, can be found here. Think tRNAscanSE, but for all types of RNA)
  • Note: we already have the Bio::SearchIO::infernal parser, the Bio::Tools::Run::Infernal wrapper, and Bio::Index::Stockholm (the latter recently committed to CVS for indexed Rfam/Pfam alignments). These can be used in a way similar to rfamscan, which runs cmsearch for every Rfam model. The parser scans Infernal 0.81 output; I plan on updating the wrapper as well when Infernal 1.0 is release (supposedly soon). --Chris Fields 23:53, 6 November 2007 (EST)

Evidence based

• Bio::Tools::Est2Genome
• Bio::Tools::ESTScan
• Bio::Tools::Genewise - also see Bio::SearchIO wise parser
• Bio::Tools::Sim4::Results - also see Bio::SearchIO sim4 parser
• Bio::Tools::Spidey::Results