Databases

Database name	Keywords	Description	Web ressources	Publications
Actinome	Actin, cytoskeleton, database	Actinome is a collection of sequences related to the cytoskeleton.	website	PMID: 17727702
Alvinella	Alvinella pompejana, Polychaete Annelid, thermostable	Alvinella pompejana, the "Pompeii worm", is a Polychaete Annelid (see taxonomy) discovered in 1980. This tubiculous worm colonizes hydrothermal vents where it is faced with extreme and variable physico-chemical conditions including very high temperatures (from 20 to over 80°C), anoxic conditions, low ph, high concentration of heavy metals and sulphids... This environment makes A. pompejana an ideal model for studies aimed at deciphering adaptation in general as well as a unique source of thermostable proteins of eukaryotic origin.	website	PMID: 20663123
Balibase version 3	Multiple sequence alignment, benchmark, reference alignment	BAliBASE is a collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins.	website	PMID: 16044462 PMID: 11125126 PMID: 10068696
Barcodes	Evolutionary barcode, protein evolutionary history, mulit-level barcode	EvoluCode is a new formalism, which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories for the human proteome.	website	PMID: 22267905
GeCoDB	Genomic context, biostatistics, boxplot radar, average gene mapping deep-sequencing	GeCoDB (Genomic Context Database) is dedicated to DNA-oriented bioinformatics and focus particularly on genomic and genic context, whether this context is intrinsec or epigenomic.	website	Ongoing
GxDb	Gene expression, Transcriptomic database	GxDb aims to collect, analyse, manage, query and display Transcriptomics Data. If you have cel files, create a new experiment with its corresponding organism, individual, samples, realexps, etc. Upload your files, run the automatic analysis ... (please, first of all, contact Laëtitia or Raymond) Then query and visualise the results.	website	Ongoing
Evi-Genoret	EVI-GENORET, Retina, Genoret Database	Genoret Database aims to centralise phenotypic, genomic and proteomic data concerning retinal diseases as well as data concerning patients. This should allow implementation of standards and permit the establishment of common information networking systems. The Genoret Database is a Relational Database whose advantage is to store heterogeneous data in a standard format. It provides an easy manual or automatic access, allowing direct deposits focused on workpackages and workpackage deliverables.	website	EVI-GENORET Integrated Project LSHG-CT-2005-512036
ICDS	Interrupted Coding Sequence, ORF	ICDS (Interrupted CoDing Sequence) are the result of unrecognized frameshifts, in-frame stop codons and sequencing errors that can seriously affect all subsequent steps of functional characterization, from in silico analysis to high-throughput proteomic projects. The Interrupted CoDing Sequence database contains ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes.	website	PMID: 16381882
MSV3d	Structural Mutation, Phenotype, Disease	MSV3d (Database of human MisSense Variants mapped to 3D protein structure) is a database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model.	website	PMID: 22491796
SM2PH-db	Structural Mutation, Phenotype, Disease	SM2PH-db (from Structural Mutation to Pathology Phenotypes in Human - database) is a relational database which gathers proteins involved in human monogenic diseases and provides for each of them a combined evolutionary and structural view coupled to mutation and phenotypic data.	website	PMID: 19921752 PMID: 20543432 PMID: 20164459
Other ...	Other links	LBGI's additional web sites.	website

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