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Accueil > Départements > Biologie des Génomes > Olivier LESPINET : Bio-Informatique Moléculaire

Logiciels

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Corbank : A fast tool for genomic comparison.
CorBank is a cross-referencing system that gives exhaustive information when matching CDS of completely sequenced replicons (chromosomes and plasmids) that have been independently reannotated in the prokaryotic curated genomic databases RefSeq (NCBI) and Genome Reviews (EBI).

Frali : A multiple alignment tool for composite proteins families.
Frali is a tool that creates accurate multiple sequence alignments (MSAs) of large and heterogeneous families comprising remote homologues. After semi-manually building an accurate MSA representative of the framework of the whole family, the user only needs to provide new homologous sequences to build the final reference MSA automatically.

FUNGIpath : A tool to assess fungal metabolic pathways predicted by orthology.
FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances.

GenRGenS : Random sequences generation.
This software is dedicated to random generation of genomics sequences that supports several classes of models, including Markov chains, HMM, context-free grammars, PROSITE patterns and more. GenRGenS is a free software under GNU license.

NestedAlign : Pairwise RNA secondary structure comparison.

Rna3Dmotif : Software for extracting RNA tertiary motifs.
Rna3Dmotif is a free bundle of three easy-to-install programs aimed to be used in combination to automatically extract recurrent RNA local tertiary motifs. The approach used is based on a graph representation of the RNA tertiary structure using LW no-menclature. It was applied to three widely studied ribosomal RNA structures and the motifs thus found were deposited in a dedicated repository

VARNA : Visualisation Applet for RNA.
VARNA is Java lightweight Applet dedicated to drawing the secondary structure of RNA. It is also a Swing component that can be very easily included in an existing Java code working with RNA secondary structure to provide a fast and interactive visualization.

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