Genostar
Encyclopedia
Genostar is a bioinformatics
solution provider based in Grenoble
, France
. The company was founded in 2004 following the "Genostar consortium" that was created in 1999 as a public-private consortium by Genome Express, Hybrigenics, INRIA (Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control) and The Pasteur Institute
.
, mapping, annotation transfer and identification of protein domains, comparative genomics
, structural searches, metabolic pathway
analysis, modeling and simulation of biological networks. Genostar's software is platform independent and can thus be used for both Mac OS X
, Windows
, and Linux
.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
solution provider based in Grenoble
Grenoble
Grenoble is a city in southeastern France, at the foot of the French Alps where the river Drac joins the Isère. Located in the Rhône-Alpes region, Grenoble is the capital of the department of Isère...
, France
France
The French Republic , The French Republic , The French Republic , (commonly known as France , is a unitary semi-presidential republic in Western Europe with several overseas territories and islands located on other continents and in the Indian, Pacific, and Atlantic oceans. Metropolitan France...
. The company was founded in 2004 following the "Genostar consortium" that was created in 1999 as a public-private consortium by Genome Express, Hybrigenics, INRIA (Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control) and The Pasteur Institute
Pasteur Institute
The Pasteur Institute is a French non-profit private foundation dedicated to the study of biology, micro-organisms, diseases, and vaccines. It is named after Louis Pasteur, who made some of the greatest breakthroughs in modern medicine at the time, including pasteurization and vaccines for anthrax...
.
Software
Metabolic Pathway Builder is a bioinformatics environment dedicated to microbial research. This streamlined bioinformatics solution covers sequence assemblySequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...
, mapping, annotation transfer and identification of protein domains, comparative genomics
Comparative genomics
Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...
, structural searches, metabolic pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
analysis, modeling and simulation of biological networks. Genostar's software is platform independent and can thus be used for both Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
, Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, and Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
.
Sequence assembly
- Mapping of an ensemble of sequences on a reference sequence
- between a reference sequence and contigs, between two sequences or between two sets of sequences
- finding of exact matches with minimum length using MUMmerMUMmerMUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes...
- detection of specific regions and SNPs
- creation of an assembled sequence relative to reference sequences
Genomic annotation
- Gene prediction: ab-initio gene prediction using a Hidden Markov modelHidden Markov modelA hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E...
based method - BlastXBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
- Automatic annotation transfer using BlastPBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
Proteic annotation
Metabolic Pathway Builder integrates several methods dedicated to proteic annotation:- PfamPfamPfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
domain prediction using HMMERHMMERHMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences. It does this by comparing a profile-HMM to either a single sequence or a database of sequences... - Several EMBOSSEMBOSSEMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
methods (antigenic, 2D structure prediction)
Expression Data Solution (EDS)
Genostar's Expression Data Solution (EDS) connects microarray data to genes, gene products and biochemical reactions, based on keywords and annotations. This software solution allows to:- Assign expression values to the gene names and IDs
- Identify co-expressed genes and visually analyze the reactions and metabolic pathwaysMetabolic pathwayIn biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
in which they are involved - Identify and perform analysis on co-regulated genes in terms of genomic localization, functional annotation and metabolism
- Colorize CDSs of interest in genomic maps according to their expression values and highlight the corresponding reactions in interactive metabolic KEGG maps
- Analyze the significance of functional data of a collection or sub-collection of CDSs (GOGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
, KEGG and more): Fisher testFisher testThe Miller Fisher test is a diagnostic procedure used to confirm suspected normal pressure hydrocephalus . The Miller Fisher test confirms NPH if the removal of 30 mL of cerebrospinal fluid results in clinical improvement of NPH symptoms.... - Collect and visualize all functional data in exportable tables and maps
Database
Genostar's MicroB database is constructed of perfectly integrated and rigorously cross-checked genomic, proteic, biochemical and metabolic data approximately 1100 bacterial and archaeal organisms.Industrial Partners
- ChemAxonChemaxonChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research...
- Pathway Solutions
- KoriLog
Academic Partners
- INRIA (Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control)
- Swiss Institute of BioinformaticsSwiss Institute of BioinformaticsThe Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland...