Site du Genoscope

Genoscope's Resources

2007-06-04T09:06:17Z

Organism	Project	Server	Article	Updating
Prokaryotes:		MaGe
Acinetobacter baylyi ADP1	Whole genome shotgun	GGB	2008	2008
Eukaryotes :
Arabidopsis thaliana	Chromosome 3	GGB	2000,	2000
	cDNA	GGB	2004	2004
Homo sapiens	Chromosome 14	GGB	2003	Fev. 2003
	Splicing alternatif	GGB	2006	Mai 2006
Oïkopleura dioica	Whole genome shotgun	GGB	2006	Fev. 2007
Paramecium tetraurelia	Whole genome shotgun	GGB	2006	Nov. 2006
Tetraodon nigroviridis	Whole genome shotgun	GGB	2004	Mars 2007
Vitis vinifera	Whole genome shotgun	GGB	2007	Sept.07
Tuber melanosporum	Whole genome shotgun	GGB	2010	Mar.2010

BLAST (Article, Link) for Basic Local Aligment Search Tool: A sequence comparison algorithm optimised for speed which is used to search sequence databases for optimal local alignments to a query.
BLAT (Article, lien) for Blast like alignment tool : An mRNA/DNA and cross-species protein sequence analysis tool to quickly find sequences of 95% and greater similarity of length 40 bases or more.
GGB for Generic Genome Browser (Article, Link): graphic interface for various databases (sequence, annotation, synténies...) for a given organism.
MaGe for Magnifying Microbial Genomes (Article, Link): annotation system for microbial genomes.

Other resources

2007-06-04T09:55:07Z

Human genetic map, supplementary data (Nature 1996)

NCBI

Genbank : GenBank® is a sequence database that contains publicly available DNA sequences for more than 170,000 different organisms. GenBank data is accessible through NCBI?s retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
UniGene UniGene provides an organized view of transcribed sequences by collapsing them into groups that correspond to genes and then connecting these entries to other classes of information that may shed light on gene expression and function. Tools provided on the UniGene web site allow researchers to browse cDNA libraries by developmental stage or tissue of origin, view surrogate expression profiles based on EST counts, and find groups of genes with similar expression patterns.

COG :The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on phylogenetic classification of the proteins encoded in complete genomes. Each COGs includes proteins that are inferred to be orthologs (direct evolutionary counterparts). The current release consists of 138,458 which form 4873 COGs and comprise 75% of the 185,505 proteins from 50 bacterial genomes, 13 archaeal genomes, and three genomes of unicellular eukaryotes. The COG database is updated periodically as new genomes become available.

EMBL The EMBL Nucleotide Sequence Database (URL : http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. Network services allow free access to the most up-to-date data collection. For sequence similarity searching a variety of tools (e.g. Fasta, BLAST) are available.

Ensembl : Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes. This site provides free access to all the data and software from the Ensembl project.

TIGR Gene Indices : Analysis of the public EST sequences, available through the TIGR Gene Indices (TGI ; http://www.tigr.org/tdb/tdb.html), is an attempt to identify the genes represented by that data and to provide functional, structural, and evolutionary information regarding those genes. Gene Indices are constructed by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or Tentative Consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

ASDB - Alternative Splicing Database : ASDB consists of two divisions, ASDB (proteins), which contains amino acid sequences, and ASDB (nucleotides) with genomic sequences. The protein entries from SwissProt are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank. The search engine allows one to search over SwissProt and GenBank fields and then follow the links to all variants.

Resources of Genoscope

2008-02-22T09:13:29Z

- Resources

Human genetic map, supplementary data (Nature 1996)

2008-06-05T14:09:03Z

This table provides direct access to tabular data and chromosome maps related to this publication :

Dib C. et al, A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380, 152 - 154 (14 March 1996); doi:10.1038/380152a0.
Abstract | PDF (Links to the Nature Website ; full text (PDF document) may require special arrangment with Nature Publishing Group).

Chromosomes	Alleles	Data	Chromosome map (PDF format)	sequences
Chr1	Allele Chr1	Data Chr1	Figure Chr1	Sequence Chr1
Chr2	Allele Chr2	Data Chr2	Figure Chr2	Sequence Chr2
Chr3	Allele Chr3	Data Chr3	Figure Chr3	Sequence Chr3
Chr4	Allele Chr4	Data Chr4	Figure Chr4	Sequence Chr4
Chr5	Allele Chr5	Data Chr5	Figure Chr5	Sequence Chr5
Chr6	Allele Chr6	Data Chr6	Figure Chr6	Sequence Chr6
Chr7	Allele Chr7	Data Chr7	Figure Chr7	Sequence Chr7
Chr8	Allele Chr8	Data Chr8	Figure Chr8	Sequence Chr8
Chr9	Allele Chr9	Data Chr9	Figure Chr9	Sequence Chr9
Chr10	Allele Chr10	Data Chr10	Figure Chr10	Sequence Chr10
Chr11	Allele Chr11	Data Chr11	Figure Chr11	Sequence Chr11
Chr12	Allele Chr12	Data Chr12	Figure Chr12	Sequence Chr12
Chr13	Allele Chr13	Data Chr13	Figure Chr13	Sequence Chr13
Chr14	Allele Chr14	Data Chr14	Figure Chr14	Sequence Chr14
Chr15	Allele Chr15	Data Chr15	Figure Chr15	Sequence Chr15
Chr16	Allele Chr16	Data Chr16	Figure Chr16	Sequence Chr16
Chr17	Allele Chr17	Data Chr17	Figure Chr17	Sequence Chr17
Chr18	Allele Chr18	Data Chr18	Figure Chr18	Sequence Chr18
Chr19	Allele Chr19	Data Chr19	Figure Chr19	Sequence Chr19
Chr20	Allele Chr20	Data Chr20	Figure Chr20	Sequence Chr20
Chr21	Allele Chr21	Data Chr21	Figure Chr21	Sequence Chr21
Chr22	Allele Chr22	Data Chr22	Figure Chr22	Sequence Chr22
ChrX	Allele ChrX	Data ChrX	Figure ChrX	Sequence ChrX

Laboratory for enzymatic cloning and screening

2009-04-20T09:25:29Z

Group members

The mission of the high throughput cloning and enzymatic screening platform includes two types of projects:

	o “ORFeome” projects: construction of the ORFeome of bacteria Acinetobacter baylyi ADP1)
	o “Biocatalysis” projects : search for biocatalysts by large-scale screening of enzyme families on panels of substrates potentially pertinent for industry.

Large-scale functional genomics project

Several years ago Genoscope started to take advantage of its savoir-faire in “high-throughput” technology to develop tools for large-scale studies of “functional genomics” for the purpose of fundamental research (enrichment of our knowledge of the function of enzymes) or the discovery of new biocatalysts which could be utilized in industry. This project fits in with the desire of Genoscope to contribute actively and massively to the inventory of chemical reactions catalyzed by microbial enzymes (UMR8030 “Metabolic Genomics”), whose sequences are accumulating in public databases.

Furthermore, enzymes whose functions have already been characterized have usually been studied in a specific metabolic context. However, it has been shown repeatedly that enzymes are less substrate-specific than previously thought, and it is not rare for an enzyme to be bi-functional or for a substrate to be the target of several metabolic enzymes with a large spectrum of activity (example: dehydrogenases). Furthermore, the screening of enzymes, even those with “known” function, on unnatural substrates should increase the catalog of possible reactions of these enzymes, even when the activity detected is marginal. In fact, the efficacy of these enzymes can then be increased by various methods of evolution (mutagenesis, evolution of strains, etc.).

Platform for enzymatic cloning and screening

Candidate enzymes for screening are most often selected by sequence homology (even those with weak homology, to augment diversity) with reference proteins (known proteins with a specific activity).

The candidate genes are amplified from DNA from a collection of strains from Genoscope and the “Cloaca maxima” metagenome, then cloned in 96-well microtiter plates by a cloning method which employs restriction and ligation enzymes (LIC).

The cloned genes are then over-expressed in E. coli BL21 in 96-well microtiter plates followed by the preparation of cellular lysates. Enzymatic screening of these plates is carried out in 96 or 384-well format.

This platform, which has been functioning for more than a year, has a current output of about 5000 clonings per year.

Group members of LCAB

2009-04-20T09:25:35Z

Project

Group leader : Véronique de Berardinis (Researcher)

Aline Mariage

Jean-Louis Petit

Agnès Pinet

Marielle Besnard-Gonnet

Adrien Debard

Virginie Pellouin

Biocatalysts

2009-04-20T09:26:07Z

LCAB project
LCAB group members

Enzymes which are capable of catalyzing reactions which have numerous advantages:

substrate specificity
srictly enantioselective and regiospecific
active under mild conditions of pH and temperature
do not require the utilization of solvents

As a result, biocatalysis reduces environmental costs of classical synthetic chemistry and participates in the development of “sustainable” chemistry which is becoming more and more important in the politics of development of industrial activities. The synthesis of chemical products thanks to biotechnology processes which use enzymes is called “white biotechnology” and is used by an increasing number of industrialists for the production of organic compounds, products for use in agriculture, pharmaceutical products, food additives and bioplastics (Hatti-Kaul et al., 2007).

Multiple implications of enzymes in industry:

Ligation Independent Cloning

2009-04-20T09:26:05Z

LCAB project
LCAB group members

The technique utilized, which is called LIC (Ligation Independent Cloning), is based on the properties of T4 polymerase and was described by Aslanidis and de Jong in 1990.

Platform for enzymatic cloning

2009-04-20T09:26:04Z

LCAB project
LCAB group members

Candidate enzymes for screening are most often selected by sequence homology (even those with weak homology, to augment diversity) with reference proteins (known proteins with a specific activity).

The cloned genes are then over-expressed in E. coli BL21 in 96-well microtiter plates followed by the preparation of cellular lysates. Enzymatic screening of these plates is carried out in 96 or 384-well format.

This platform, which has been functioning for more than a year, has a current output of about 5000 clonings per year.

Collection of prokaryote strains

2009-04-20T09:26:02Z

LCAB project
LCAB group members

The number of prokaryotic genomes sequenced has been progressing exponentially for several years and it is estimated that for each of these new genomes, 1/3 of the genes have an unknown function. This ensemble of data is therefore a precious resource to be explored.

Number of genomes sequenced per Years :

Genoscope is thus creating a collection of strains in constant progression which presently includes more than 300 bacterial and archaeal genomes.

We also use metagenomic DNA from the anaerobic digester of the Evry Wastewater Treatment Plant (“Cloaca Maxima” project of LMP), which has been sequenced at Genoscope and which provides access to several thousand genes, most of which are from bacteria which are still unknown.