AUGUSTUS -- ab initio prediction of alternative transcripts

What you can do:
Predict gene in eukaryotic genomic sequences based on a generalized hidden Markov model.
Highlights:
  • The web server allows the user to impose constraints on the predicted gene structure.
  • A constraint can specify the position of a splice site, a translation initiation site or a stop codon.
  • Furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence.
  • The number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure.
  • The result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. The specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction.
  • The web interface and the downloadable stand-alone program are available.
  • In the updated 2006 release, the server is able to predict multiple splice variants.
  • In addition, a motif searching facility allows search of user-defined regular expressions against putative proteins encoded by the predicted genes.
Keywords:
  • gene prediction tool
  • gene discovery tool
  • gene scan tool
  • gene structure prediction tool
  • multiple splice variants prediction tool
  • gene splicing prediction tool
  • gene identification tool
  • eukaryotic gene prediction
  • human gene prediction tool
  • Drosophila gene prediction tool
  • Arabidopsis gene prediction tool
  • Brugia gene prediction tool
  • Aedes gene prediction tool
  • Coprinus gene prediction tool
  • Tribolium gene prediction tool
This record last updated: 11-22-2005

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