FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.
BACKGROUND
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.


CONCLUSIONS
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.


BACKGROUND
The program is developed as a stand-alone Java application, and is available as GPLv3 open-source software. The program, source and documentation can be obtained from the 'Software' section at http://bioinformatics.psb.ugent.be/.


BACKGROUND
Supplementary data is available at Bioinformatics online.
Van Bel
Michiel
M
Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.
Saeys
Yvan
Y
Van de Peer
Yves
Y
D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004247:DNA