Related Experiment Video
Updated: Jul 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA
Michiel Van Bel1, Yvan Saeys, Yves Van de Peer
1Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.
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. The program, source and documentation can be obtained from the 'Software' section at http://bioinformatics.psb.ugent.be/.
Supplementary Information:
Supplementary data is available at Bioinformatics online.
More Related Videos
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Modern Molecular Taxonomy
Functional Classification of Joints
The functional classification of joints is determined by the amount of mobility between the adjacent bones. Joints are functionally classified as a synarthrosis or immobile joint, an amphiarthrosis or slightly moveable joint, or as a diarthrosis, a freely moveable joint. Fibrous and cartilaginous joints can be functionally classified as either synarthroses or amphiarthroses, whereas all synovial joints are classified as diarthroses.
Synarthrosis
An immobile...
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Ligand Binding and Linkage
Predicting Molecular Geometry

