• Genomes
  
• Nucleic databases
  
• Protein Databases
  
• SRS
  
• Other databases
  

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Genomes

	Name	Description	Link
	AcinetoCyc	A pathway genome database dedicated to Acinetobacter baylyi ADP1	AcinetoCyc online
	Bacillus Subtilis complete genome		Pasteur’s webpage
	Borrelia burgdorferi complete genome		Pasteur’s webpage
	Caenorhabditis elegans complete genome		Pasteur’s webpage
	Chlamydia pneumoniae complete genome		Pasteur’s webpage
	EMGLib	database devoted to the completely sequenced bacterial genomes and the yeast genome.	website
	Ensembl	a software system which produces and maintains automatic annotation on selected eukaryotic genomes	ENSEMBL website
	Ensembl for SIGENAE	Ensembl : Sigenae EST ContigBrowser (Bos taurus, Gallus gallus, Oncorhynchus mykiss, Sus scrofa, Oryctolagus cuniculus)	Sigenae EST ContigBrowser
	Escherichia coli complete genome		Pasteur’s webpage
	FLAGdb++	Integrative database around plant genomes	homepage
	GeM	a comparative mapping database dedicated to all vertebrate complete genome including SNP data detected from ESTs	GeM homepage
	Genolevures	tools and data relative to 4 complete genome sequences and 10 partial genome sequences	website
	GenoList genome browser	a browser for 21 bacterial genomes	Pasteur’s webpage
	Helicobacter pylori complete genome		Pasteur’s webpage
	Homolens	a database of homologous genes from Ensembl fully sequenced organisms, it allows one to visualize multiple alignments and phylogenetic trees.	Homolens homepage
	Human Genome Browser		Databases in Lille
	IMGT/GENE-DB	Database of immunoglobulin and T cell receptor genes	webpage
	MaGe	Magnifying Genomes - Microbial Genome Annotation System	MaGe homepage
	MICADO	microbial genomes and functional analysis of Bacillus subtilis	website
	MolliGen	a database dedicated to the comparative genomics of Mollicutes	webpage
	MOSAIC	a relational database and web interface developed to compare closely related bacterial genomes	Mosaic online
	Mycobacterium tuberculosis complete genome		Pasteur’s webpage
	Mycoplasma Genitalium complete genome		Pasteur’s webpage
	Mycoplasma Pneumoniae complete genome		Pasteur’s webpage
	Paramecium genome browser		Paramecium server
	Ralstonia solanacearum Strain GMI1000		website
	RicBase	Rickettsia genome database	website
	Sinorhizobium meliloti strain 1021		website
	Tetraodon genome browser	browse the smallest genome known to date in the vertebrates	Tetraodon genome browser
	Tropheryma whipplei genome database	human pathogen Tropheryma whipplei is the only known reduced genome species (<1 Mb) among the Actinobacteria	website
	Yeast chromosomes		Pasteur’s webpage
	Yersinia pestis unfinished genome		Pasteur’s webpage

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Nucleic databases

	Name	Description	Link
	ACNUC	Retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence databases SWISS-PROT or NBRF.	ACNUC webpage
	BIBIDB	a nomenclature and taxinomy driven bacterial DNA sequences database used in bacteria identification
	BIGS	Bacterial targets database	website
	Cardiac genes database	Heart-specific genes revealed by expressed sequence tag (EST) sampling	Homepage
	Embl	EMBL Nucleotide Sequence Database	Pasteur’s webpage
	FamFetch	the general interface used to query the families databases developed using the HOBACGEN model	FamFetch webpage
	FlyGATE	Drosophila melanogaster knowledge database : Genome Analysis for Transposable Elements	FlyGATE’s homepage
	GenBank	the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.	GenBank at NCBI
	GOLDEN	A tool to search the nucleic and proteic databases.	webpage
	HCVDB	The aim of Hepatitis C Virus DataBase is to establish correlations between virus sequences and pathology.	website
	Hogenom	database of homologous genes from fully sequenced organisms, structured under ACNUC sequence database management system	Hogenom webpage
	Hoppsigen	a nucleic database of homologous processed pseudogenes	Hoppsigen webpage
	Hovergen	Homologous Vertebrate Genes Database	Hovergen webpage
	IMGT/LIGM-DB	a comprehensive database of Immunoglobulins and T cell Receptors from human and other vertebrates	webpage
	NuReBase	bioinformatic database of nuclear receptors	NuReBase website
	Polymorphix	a database of intraspecific sequence polymorphism, structured under the ACNUC sequence database management system	Polymorphix webpage
	REBASE	Restriction enzymes cut sites database	Rebase webpage
	RefSeq	set of sequences, including genomic DNA and transcript (RNA), for major research organisms.	RefSeq at NCBI
	TaxoBacGen	a taxonomic genomic database, structured under ACNUC sequence database management system
	Unigene	experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.	Unigene at NCBI
	Utr	Untranslated regions of eukaryotic mRNAs	Pasteur’s webpage
	Vector	Vector subset of GenBank(R), NCBI	Pasteur’s webpage

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Protein Databases

	Name	Description	Link
	ACNUC	Retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence databases SWISS-PROT or NBRF.	ACNUC webpage
	AliasServer	a web server to handle multiple aliases used to refer to proteins	homepage
	Balibase & Balibase2	manually-refined multiple sequence alignments specifically designed for the evaluation and comparison of multiple sequence alignment programs.	webpage
	Blocks	Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins	Blocks home
	Décrypthon	the result of the first comprehensive comparison (Smith-Waterman) of all known proteins.	Decrypthon at Infobiogen
	DOMO	multiple sequence alignments including protein domains as well as repeating sequence regions extracted from non-redundant molecular primary structures contained in the SWISS-PROT and PIR databases	webpage
	ESTHER	analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases	webpage
	FamFetch	the general interface used to query the families databases developed using the HOBACGEN model	FamFetch webpage
	Genpept	Translations of Genbank	Pasteur’s webpage
	GOLDEN	A tool to search the nucleic and proteic databases.	webpage
	HCVDB	The aim of Hepatitis C Virus DataBase is to establish correlations between virus sequences and pathology.	website
	Hogenom	database of homologous genes from fully sequenced organisms, structured under ACNUC sequence database management system	Hogenom webpage
	Interpro	Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.	EBI’s webpage
	IPRMatches	List of precomputed matches of Interpro entries in Swissprot and TrEMBL.	EBI’s webpage
	Nrl3d	Sequence and annotation extracted from PDB	Pasteur’s webpage
	Nrprot	NCBI non-redundant: Genbank CDS translations+PDB+Swissprot+PIR	Pasteur’s webpage
	NuReBase	bioinformatic database of nuclear receptors	NuReBase website
	Pfam	A Collection of Protein Domain Families	Pfam at Sanger
	PRDB	large-scale analysis of protein tandem repeats	PRDB
	Prints	Protein Motif Fingerprint Database	Prints home
	Prodom	A protein domain database which consists of homologous domains detected in the SWISS-PROT database	Prodom home
	PROSE	The relational database PROSE contains protein sequences from Swissprot, Trembl and Trembl_New	webpage
	Prosite	Dictionary of Protein Sites and Patterns	Prosite home
	RefSeqP	a comprehensive, integrated, non-redundant set of protein sequences for major research organisms.	RefSeq at NCBI
	RTKdb	database containing all the protein sequences of Receptor Tyrosine Kinase, organized into families	webpage
	SBase	A Collection of Annotated Protein Domain Sequences	Pasteur’s webpage
	Swissprot	SWISS-PROT Annotated protein sequence database	Swiss-prot home
	Uniprot	Universal Protein Resource = Swiss-Prot + TrEMBL + PIR	Uniprot home

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SRS

	Name	Description	Link
	SRS at Pasteur Paris		LION’s website
	SRS in Strasbourg		LION’s website
	SRS in Toulouse		LION’s website

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Other databases

	Name	Description	Link
	Alu	Select Alu repeats from REPBASE	Pasteur’s webpage
	BioFloWeb	displays a gene report containing data provided by Planet BioMoby web services about A. Thaliana genes	BioFloWeb request
	Enzyme	EC number, Recommended name, Alternative names, Catalytic activity, Cofactors, Pointers to the SWISS-PROT entrie(s) that correspond to a given enzyme	Enzyme home
	Epd	Eukaryotic Promoter Database	Pasteur’s webpage
	FusionDB	a database of bacterial and archaeal gene fusion events	FusionDB online
	IMGT/PRIMER-DB	Database of immunoglobulin and T cell receptor oligonucleotides	webpage
	INTEGRALL	database search engine for integron integrases and gene cassettes	INTEGRALL home page
	SIReGal	Plant Genetic Resources Information System	SIReGal website
	Taxonomy	List of the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.	Taxonomy at NCBI
	Transfac	Transcription Factor Database	Pasteur’s webpage

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