Symbiose Project Team - INRIA/Irisa

Software

GenOuest, Bioinformatics computing center of Ouest-genopole

The team transfers his results to the GenOuest, bioinformatics computing center of Ouest-Genopole. hosted by the team. All our developments are progressively made available within a service platform. This platform has a strategic role in the genopole, offering access to various softwares and databases. It allows our team to filter from routine service requests new subjects of research with a good relevance in biology. We propose original tools for complex filtering of sequences.

Softwares

Most of the softwares introduced here are available on the GenOuest platform.

Administration of data banks

BIOMAJ: Administration of data banks. A workflow engine dedicated to data synchronization and processing.The Software automates the update cycle and the supervision of the locally mirrored databank repository. The software automates the update cycle and the supervision of the locally mirrored databank repository. http://biomaj.genouest.org/

Sequence alignement and comparison

Tuiuiu : preliminary step before applying a multiple local aligner tool Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py?form=tuiuiu
GASSST: mapping short reads to full genomes. http://www.irisa.fr/symbiose/projects/gassst/
PLAST: intensive bank sequence comparison with a parallel version of BLAST-like software. http://www.irisa.fr/symbiose/projects/plast/

Genomes

kisSnp: SNP identification: a tool to find SNPs by comparing two sets of raw NGS reads without assembly nor mapping on a reference genome http://alcovna.genouest.org/kissnp/
Cassis: rearrangement breakpoints. Cassis is a software for precise detection of rearrangement breakpoints in whole (sequenced and assembled) genomes. http://pbil.univ-lyon1.fr/software/Cassis/
Module organizer: segmentation of DNA sequences ModuleOrganizer is a software package proposing a synthetic view of a set of DNA sequences by providing both a segmentation of them into domains and a classification on the basis of these domains. http://moduleorganizer.genouest.org
CRISPR identification CRISPI is a user-friendly web interface with many graphical tools and facilities allows extracting CRISPR, finding out CRISPR in personal sequences or calculating sequence similarity with spacers. http://crispi.genouest.org
Logol Logol is a language and a tool to define biological patterns to look for in one or more sequences (dna/rna/proteins). Patterns can be complex: the tool allows the use of variables to look for repetitions for example, the use of gaps and morphisms (reverse word complement for example), etc... http://www.genouest.org/spip.php?article758

Proteins

A_purva: Scoring similarities between proteins A_purva is a Contact Map Overlap maximization (CMO) solver. Given two protein structures represented by two contact maps, A_purva computes the amino-acid alignment which maximize the number of common contacts. http://apurva.genouest.org
Protomata-Learner Protomata-Learner infers graphical models (automata) of functional or structural families of proteins from a sample of (unaligned) sequences of the family. These models can be used to get new insights into the family, when classical multiple sequence alignments are insufficient, or to search for new family members in the sequence data banks, with the advantage of a finer level of expressivity than classical sequence patterns (such as PSSM, Profile HMM, or Prosite Patterns). http://protomata-learner.genouest.org/

Systems biology

Bioquali: confront knowledge-based regulatory models with data Bioquali tests the consistency between an interaction graph and transcriptomic data. It outputs nodes in the network whose variation cannot be globally explained by the other available observations Bioquali as a Plugin for Cytoscape allows us to visualize the inference and consistency analyses. http://bioquali.genouest.org

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