| Database name | Keywords | Description | Web ressources | Publications |
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Actin, cytoskeleton, database |
Actinome is a collection of sequences related to the cytoskeleton. |
website |
PMID: 17727702 |
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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 |
version 3 |
multiple sequence alignment, benchmark, reference alignment |
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 |
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Genomic context, biostatistics, boxplot radar, average gene mapping deep-sequencing |
The Genomic Context Database (aka GeCoDB) website is dedicated to DNA-oriented bioinformatics and is more especially focusing on genomic and genic context, whether this context is intrinsec or epigenomic. |
website |
Ongoing |
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Gene expression, Transcriptomic database |
The aim of GxDb is 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 |
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EVI-GENORET, Retina, Genoret Database |
The aim of the Genoret Database is 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 |
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Interrupted Coding Sequence, ORF |
Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterization, from in silico analysis to high-throughput proteomic projects. Here, we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes. |
website |
PMID: 16381882 |
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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 |
