Program description : Motivation
Many problems in genome annotation are tackled by using a classification model to predict functional sites such as splice sites,
translation start sites or stop codons. Locating the correct position of these sites remains one of the most important but also one of the most difficult issues in the structural annotation of genomes.
Most of the software currently in use is written for a very specific problem, thereby limiting the possibilities for reuse.
Summary
We developed a software platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach
towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in
the human and Arabidopsis thaliana genome.
Availability
The program is developed as a stand-alone Java application, and is available as GPLv3 open-source software.