Genostar is a

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

provider based in

Grenoble lat, Gratianopolis , commune status = Prefecture and commune , image = Panorama grenoble.png , image size = , caption = From upper left: Panorama of the city, Grenoble’s cable cars, place Saint- ...

France France (), officially the French Republic ( ), is a country primarily located in Western Europe. It also comprises of Overseas France, overseas regions and territories in the Americas and the Atlantic Ocean, Atlantic, Pacific Ocean, Pac ...

. 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 The National Institute for Research in Digital Science and Technology (Inria) () is a French national research institution focusing on computer science and applied mathematics. It was created under the name ''Institut de recherche en informatiq ...

(Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control) and The Pasteur Institute.

Software

Metabolic Pathway Builder is a bioinformatics environment dedicated to microbial research. This covers

sequence assembly In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one ...

, mapping, annotation transfer and identification of

protein domains In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of s ...

comparative genomics Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...

, structural searches,

metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reac ...

analysis, modeling and simulation of biological networks. Genostar's software is

platform independent In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software r ...

and can thus be used for both

Mac OS X macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

, and

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

Sequence assembly

*Mapping 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

MUMmer Mummers' plays are folk plays performed by troupes of amateur actors, traditionally all male, known as mummers or guisers (also by local names such as ''rhymers'', ''pace-eggers'', ''soulers'', ''tipteerers'', ''wrenboys'', and ''galoshins''). ...

*detection of specific regions and

SNPs In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...

*creation of an assembled sequence relative to reference sequences

Genomic annotation

* Gene prediction: ab-initio gene prediction using a

Hidden Markov model A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an ob ...

based method * BlastX * Automatic annotation transfer using BlastP

Proteic annotation

Metabolic Pathway Builder integrates several methods dedicated to proteic annotation: *

Pfam Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families. Uses ...

domain prediction using

HMMER HMMER 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, and to perform sequence alignments. It detects homology by comparing ...

* Several

EMBOSS EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of ...

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 allows to: * Assign expression values to the gene names and IDs * Identify co-expressed genes and visually analyze the reactions and

s 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 KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...

maps * Analyze the significance of functional data of a collection or sub-collection of CDSs ( GO, KEGG and more): Fisher test * Collect and visualize all functional data in exportable tables and maps

Database

Genostar's MicroB database consists of genomic, proteic, biochemical and metabolic data from approximately 1100 bacterial and archaeal organis.

Partners

(Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control) *

Swiss Institute of Bioinformatics The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland. The institute was established on 30 March 1998 and its mission is to provide core bioinfor ...

* ChemAxon

Notes and references

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External links

Genostar Expands Deal with Biopharma Merial To Help Hunt Pathogenic Virulence Factors

Genostar at Bio 2010
Software companies of France Software companies established in 2004 Biotechnology companies of France Bioinformatics companies Privately held companies of France Science and technology in Grenoble Biotechnology companies established in 2004 2004 establishments in France