Database Software
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

 
Programs PDF Print E-mail

 

Software name Keywords Description Web ressources Logo Publications
AlexSys

Multiple Alignment, Data mining, Machine learning, UIMA, Knowledge based system AlexSys (Alignment Expert System) is a knowledge-based expert system for the construction and analysis of Multiple Sequence Alignments (MSA). The prototype uses a decision tree machine learning algorithm to automatically select a suitable MSA program for a given set of sequences. website PMID:18971242
PMID: 20530533
ARPAnno
ARP, Actin related proteins, prediction ARPAnno (Actin Related Proteins Annotation server) is a web tool that automatically annotates protein sequences according to the ARP classification.

In maintenance

website

PMID: 16195354
BBS
BBS, MSA, alignment, Bardet Biedl Syndrome Bardet-Biedl Syndrome Bioinformatics resource. website PMID: 20177705
PMID: 16823392
PMID: 17160889
PMID: 16582908
CADO4MI
Oligonucleotide design, probe design, microarray, DNA chips CADO4MI (Computer Assisted Design of Oligonucleotide 4 MIcroarray) is a program for automatic design of oligonucleotides, fully customizable and accessible through a graphical user interface. For an input set of sequences, it allows parameter optimization and can combine multiple designs in distinct sequence databases. website PMID: 17727702

Gscope

Genomics, integrative software plateform Gscope is an integrated platform allowing the analysis of all kind of genomic data. It is written in Tcl/Tk and runs on all plateforms. It is specially designed to perform high throughput analysis. Gscope is mainly composed of tools necessary to create the basic data, analysis tools, visualisation interfaces. It allows also the creation and feeding of SQL relational databases and the quering and display of the available information through a web based interface (Wscope). Gscope server Gscope
KD4v
Structural Mutation, Phenotype, Disease KD4v (Comprehensible Knowledge Discovery System for Missense Variant) allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. The rules are interpretable by non-expert humans and can be used to accurately predict the deleterious/neutral status of an unknown mutation. website KD4v PMID: 22641855
MACSIMS
Protein family analysis, multiple sequence alignment, sequence annotation MACSIMS (Multiple Alignment of Complete Sequences Information Management System) is a multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is mined automatically from the public databases. In the MACS, homologous regions are identified and the mined data is evaluated and propagated from known to unknown sequences with these reliable regions. MACSIMS provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist.

In maintenance
PMID: 16792820
OrthoInspector
Orthology, Inparalogy, Vizualisation OrthoInspector is a software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. IIn addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert. website

PMID: 21219603

PipeAlign
Protein family analysis, multiple sequence alignment, database search PipeAlign is an on-line protein family analysis tool providing both interactive and automatic workbench for the validation, integration and presentation of the biological insights resulting from the analysis. It integrates a 5 step process ranging from the search for sequence homologues in protein sequence and 3D structure databases to the definition of the hierarchical relationship between and within subfamilies. Each step relies upon the results from the previous ones until a validated multiple alignment integrating subfamilies information is produced. The Pipe can also be started from any point and intermediate results are easily consulted.

In maintenance

PMID: 12824430

RReportGenerator

automatic report, statitical analysis, R, Bioconductor, microarray, TCA RReportGenerator provides a simple and user-friendly graphical user interface (GUI) allowing to run routine statistical analysis using R via predefined analysis scenarios in a local and independent manner. Of course, the large variety of additional libraries on CRAN and Bioconductor may be used with the analysis scenarios. The results (text, figures and tables) are automatically assembled into a report in pdf- (or dvi) format. This may be accompanied by an additional file(s) for exporting (specific) results to other applications (spread-sheet programs, web-browser etc). website

RReportGenerator

PMID: 18037684
 
Other PDF Print E-mail
Name Keywords Description Web ressources Logo Publications
CDAO
ontology, evolutionary analysis CDAO (Comparative Data Analysis Ontology) provides extensive conceptual coverage of commonly used concepts in evolutionary analyses in a single framework. It is developed in collaboration with a group of domain scientists specialising in phylogenetic analysis software, the EvoInfo working group (http://evoinfo.nescent.org) . CDAO is used in a number of projects, including nexML, Nexplorer3, TreeBASE, phyloXML. website
sourceforge
PMID: 19812726