FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA
Authors : Michiel Van Bel, Yvan Saeys and Yves Van de Peer
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Program description :
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.
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.
The program is developed as a stand-alone Java application, and is available as GPLv3 open-source software.
Additional File 1 – Zip file of the FunSiP program
This file is the archive containing the FunSiP program.
Additional File 2 – Manual and documentation of FunSiP
This file contains the manual and some extra documentation of FunSiP.
Additional File 3 – Zip file containing the source code of FunSiP
This archive contains all the source code files of FunSiP.
Additional File 4 – Zip file containing pre-built models
This archive contains some pre-built models (Arabidopsis thaliana, human, Melampsora and tomato), together with the
configuration files that were used to create these models, and with configuration files that can be used to evaluate
DNA-sequences with these models.
Additional File 5 – Zip file containing training data
This archive contains the training data files that were used to generate the classification models.
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