Genostar is a

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

provider based in

Grenoble Grenoble ( ; ; or ; or ) is the Prefectures in France, prefecture and List of communes in France with over 20,000 inhabitants, largest city of the Isère Departments of France, department in the Auvergne-Rhône-Alpes Regions of France, region ...

France France, officially the French Republic, is a country located primarily in Western Europe. Overseas France, Its overseas regions and territories include French Guiana in South America, Saint Pierre and Miquelon in the Atlantic Ocean#North Atlan ...

. 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 French Institute for Research in Comp ...

(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 g ...

, 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 se ...

comparative genomics Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach c ...

, structural searches,

metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and Metabolic intermediate, intermediates of an enzymatic reaction are known as metabolites, which are ...

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

platform independent Within 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 softw ...

and can thus be used for both

Mac OS X macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

, and

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

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 were bands of men and women from the medieval to early modern era who (during public festivities) dressed in fantastic clothes and costumes and serenaded people outside their houses, or joined the party inside. Costumes were varied and mi ...

*detection of specific regions and

SNPs In genetics and bioinformatics, 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 ...

*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 Markov model in which the observations are dependent on a latent (or ''hidden'') Markov process (referred to as X). An HMM requires that there be an observable process Y whose outcomes depend on the outcomes of X ...

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 latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is cur ...

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 c 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 sequence ...

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 ...

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 bioinform ...

* 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 French companies established in 2004