Databases PDF Print E-mail
Database name Keywords Description Web ressources LogoPublications
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

Alvinella

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 BAliBASE III 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 EvoluCode 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

GeCo

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

GxDb

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

GenoretDatabase

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

ICDS

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

MSV3d

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

SM2PH-db

PMID: 19921752
PMID: 20543432
PMID: 20164459

Other ...

Other links LBGI's additional web sites. website

SM2PH-db