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.
|
|
