Softwares

This section describes some softwares on which I worked these last years.

Protein structure prediction

FT
Implementation of the Fourier transform for the analysis of periodic patterns in amino acid or DNA sequences.
PRED-TMR
Implementation of a method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (`edges', starts and ends) of transmembrane regions
PRED-TMR2
enhanced version of PRED-TMR with protein classification capabilities. The software uses an artificial neural network to filter out proteins that are not membrane proteins before processing of the input sequence to detect transmembrane domains
OrienTM
topology prediction of transmembrane proteins and segments
PRED-CLASS
a system of cascading neural networks that classifies any protein into one of four possible classes: membrane, globular, fibrous, mixed
CoPreTHi
a tool that combines the results of several transmembrane prediction algorithms into a joint prediction histogram
Dam-Bio
an integrated environment to support protein sequence and structure analysis
DB-TMR
a database of transmembrane regions automatically extracted from the SwissProt database
DB-NTMR
a database of inter-transmembrane regions automatically extracted from the SwissProt database

Gene expression analysis

CGGA
Implementation of the Co-expressed Gene Groups Analysis algorithm for extracting bi-clusters of co-expressed genes from integrated gene expression data and gene annotations obtained from biological knowledge
GenMiner
application for extracting the equivalence classes and the Informative Basis of association rules from genomic data
Thea
an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base

Semantic data integration and management

AllOnto
a Knowledge Base System capable of storing and performing queries on a large set of RDF/OWL specifications
Thea-interact
an online tool allowing the analysis of Drosophila's reactome
Thea-online
a web portal, using Semantic Web technologies to integrate, query and display information originating from several different sources

Text Mining

GeniaJ
a Java implementation of the Genia tagger (Part-of-speech tagging and shallow parsing for biomedical texts) version 3.0.1 of April 16 2007

XML document editing

keTuK
KeTuK is a Java based toolkit allowing applications to map XML documents with a set of Java Beans.