IMGT Bloc-notes

Tools

See also Tools in the The IMGT Immunoinformatics page

Search of motifs: MOTIF, ProfileScan, SMART

AnDom, Annotation of domains.
ALIGN at GENESTREAM.
Analyse amino acid sequence, PROTEININFO, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry.
Analyse des données d'expression.
Argo, The Argo Genome Browser, Broad Institute, for visualizing and manually annotating whole genomes. Standalone Java application.
ARLEQUIN, a software for population genetics data analysis (to be downloaded).
Biocatalog, EBI, Hinxton, U.K., a directory of molecular biology and genetic programs.
Biological and Biochemical Software - Infochem Ltd - Links for Chemists.
Biology WorkBench, provides a point and click interface for rapid access of biological databases and analysis tools.
BLAT at UCSC Genome Bioinformatics.
BLAST, Basic Local Alignment Search, NCBI.
BLAST at Institut Pasteur, Paris.
BLAST2 at EBI.
BLAST2 at Institut Pasteur, Paris.
BLASTULA, the BLAST programs Unprecedented Large Archive - A server of biological Blast Servers -Access to BLAST searches operating on specialised sequence databases.
BR's Crystallographic Web Applets, by Bernhard Rupp.
Calculation of Chi-square test for deviation from Hardy-Weinberg equilibrium.
Chemistry Software - Infochem Ltd - Links for Chemists.
Chime Resources.
CLUSTALW at EBI, program for generating sequence alignments.
Color menu IMGT, IMGT color menu for amino acids, tables, regions and domains.
Color menu of the Swiss-Pdb Viewer.
Comparison guide between GCG and EMBOSS.
EBI Molecular Biology Software Archive, a very large collection of free software for molecular biologists.
EMBL WWW Gateway to Isoelectric Point Service, Isoelectric Point determination.
EMBOSS: The European Molecular Biology open Software Suite. Aims to develop and integrate a range of currently available packages and tools for sequence analysis into a general, publicly available, suite of programs and libraries.
EndNote: la gestion facile des bibliographies, logiciel de gestion de références bibliographiques insérées dans un texte.
EndNote: Bibliographies Made Easy!, software for the management of bibliographical references.
Entrez, NCBI, WWW browser which contains searchable indexes of the MEDLINE, PubMed and GenBank databases.
ESEfinder.
ExPaSy Proteomic tools.
FASTA at Institut Pasteur, Paris.
FBAT, Family Based Association Testing software .
Fisher's Exact Test.
GeneDoc, a multiple sequence alignment editor which allows various display formats.
GeneNet, The GeneNet system is designed for formalized description and automated visualization of gene networks. The GeneNet system includes: database on gene network components, Java program for the data visualization. http://www.bioinfo.de/isb/2002/02/0009/.
Genetic Linkage Analysis at Rockefeller University.
Genetics software, two free programs for downloading: MapDisto for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. One of its specificities is to propose recombination fraction estimates in case of segregation distortion. CSSL Finder for managing introgression lines, and particularly useful to develop Chromosome Segment Substitution Lines (CSSLs).
Genomic Object Net, software tool for biopathway modeling ans simulation.
Genotator, a workbench for sequence annotation and annotation browsing, runs on Unix workstation.
GENSCAN.
HGMP-RC, UK Human Genome Mapping Project - Resource Centre Bioinformatics, access to a comprehensive range of programs and databases to aid genomic and proteomic research.
IMGT/Allele-Align, LIGM.
IMGT/JunctionAnalysis, analysis of the immunoglobulin (IG) and T cell receptor (TR) V-J and V-D-J junctions, LIGM.
IMGT/PhyloGene, LIGM.
IMGT/V-QUEST, sequence alignment software for immunoglobulins (IG) and T cell receptors (TR), LIGM.
IMGT Collier de Perles
IMGT/DomainDisplay
IMGT/DomainGapAlign
IMGT/DomainSuperimpose
IMGT/StructuralQuery
IMGTNucleic Acid Multiple Sequence Analysis, HGMP UK.
InstaSeq,developed by the Bioinformatics and Computational Biosciences Unit (BCBU) at the Georgetown University, a Google powered search engine that locates a nucleotide or amino acid sequence from the Web (30-75 characters; spaces and numbers OK).
Introduction to ELISA Activity. The Biology Project. Immunology.
IUBio Archive for Biology data and software, an archive of biology data and software in the field of molecular biology.
LALIGN.
LIGPLOT, Program for automatically plotting protein-ligand interactions. Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts (available free to academic institutions by anonymous ftp).
Logiciels pour la Biologie - Institut Pasteur.
LPC, Ligand-Protein Contacts.
LVB 1.0, Reconstructing evolution with parsimony and simulated annealing.
Mat Inspector: Search for transcription factor binding sites.
MaxSprout, algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.
Méthodes physiques de séparation et d'analyse et méthodes de dosage des biomolécules René Lafont Jussieu 2002
- Techniques chromatographiques.
- Techniques électrophorétiques.
- Techniques spectroscopiques.
- Techniques immunologiques.
Molecular weight from sequence.
MoLGraph, Molecular Graphics with POVRay and Swiss PDB Viewer.
MolProbity, Evaluate X-ray, Evaluate NMR, Work with kinemages
MOTIF - Protein Sequence Motif Search.
Multiple Sequence Alignments, BCM Search Launcher.
Multalin, Multiple sequence alignment.
MView, multiple alignment viewer.
Naccess, Atomic Solvent Accessible Area Calculations. Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids (available free to academic institutions).
NBIF - Biotechnology Software, National Biotechnology Information Facility, links to biotechnology related non-commercial software available via the Internet.
NetOGlyc, neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
Noncovalent Bond Finder (NCBF), a software to visualize hbonds or hydrophobic contacts. This tool requires Chime 2 and Netscape Navigator 4.04 or later (4.6 recommended).
PAUP, PhylogeneticAnalysis Using Parsimony, a software used for determining the inference of evolutionary trees.
PBAT, Tools for the statistical analysis of family-based association studies.
PDB Lite for searching and downloading macromolecules. PDB Lite is designated for nonspecialists who search for atomic coordinate ("PDB") files at the Protein Data Bank on an occasional basis.
pDRAW32 DNA analysis software, by AcaClone software, a freeware DNA cloning, sequence analysis and plasmid/DNA plotting software.
PHYLIP, PHYLogeny Inference Package, program for generating phylogenetic trees.
Phylo-Win, a graphical colour interface for molecular phylogenetic inference, at PBIL, Lyon (France).
Phylogeny.fr
Phylogeny programs, Joe Felsenstein's list.
Predicting Protein-3D structures based on homologous sequence search.
Primer3, primer pair designing .
ProfileScan, search a protein sequence against a profile database.
Protein Explorer (PE), a visualization freeware which offers a RasMol-like interface in Chime (require Netscape version 4.04 or later, and Chime 2.0).
Protein structure verification - WHAT IF check.
ProtoNet, an automatic classification of protein sequences based on hierarchical clustering.
PSORT, Prediction of Protein SORTing Signals, a computer program for the prediction of protein localization sites in cells.
QTL Viewer, visualises the physical position of QTLs for both the human and mouse genomes. Features of the tool include the ability to estimate the size of a QTL and the display of overlapping QTLs.
RasMol, Molecular Visualization Freeware.
Reactome - a knowledgebase of biological processes. Reactome covers biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signalling, mainly targeted at human pathways, but also includes rat, mouse, fugu fish and zebra fish. Reactome supersedes and incorporates all the information from The Genome Knowledgebase.
- Download Reactome data and code, Export of human reactions in Systems Biology Markup Language (SBML) Level 2.
RECUE ESE, An online tool for identifying candidate ESEs in vertebrate exons.
Reverse Complement of Sequence.
Reverse Translator, DNA point mutations and amino acid substitutions.
SEQUEROME, developed by the Bioinformatics and Computational Biosciences Unit (BCBU) at the Georgetown University, a tool performing detailed analysis of an input sequence. All the analysis and manipulation is done within a single browser session; user tracks his analysis history as icons in a separate panel .
Service des concours agronomiques.
Signal Peptide Prediction.
SignalP - Prediction of signal, a program for the prediction of the presence and location of signal peptide cleavage sites in amino acid sequences.
SMART, Simple Modular Architecture Research Tool, identification and annotation of domains from signalling and extracellular protein sequences.
Splign, NCBI spliced-alignment tool.
START (Sequence Type Analysis and Recombinational Tests), a selection of tools useful in the analysis of MLST data. These tools can be broadly divided into four categories: data summary, lineage assignment, tests for recombination, tests for selection. MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet).
StrucTools, Common structural biology calculations. Calculates surfaces , B-factor plots, hydrogen bonds and secondary structure from a PDB coordinate file.
SURFNET, the SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file. It can compute: van der Waals surfaces, Gap regions between molecules, Clefts, cavities and protein binding sites, 3D density distributions and sidechain-sidechain interactions (available free to academic institutions by anonymous ftp).
Swiss-Pdb Viewer.
Tandem repeats finder.
TESS, Transcription Element Search Software.
TFSEARCH: Searching Transcription Factor Binding Sites, Japan.
The Ka/Ks service.
Toolbox at the EBI.
Transeq (EMBOSS) translates nucleic acid sequences.
Translate tool, ExPaSy.
TreeDyn, a dynamic graphics editor for exploring phylogenetic or classification trees, at IRF, Montpellier (France).
TreeView
UCSF Chimera.
Webcutter.
WebLogo, Generation of sequence logos.
Web server for Protein structure Comparison, Pairwise/Multiple alignment and similarity search in databases for three dimensional protein structures.
WIT, Argonne National Labs, a www-based system designated for supporting the curation of gene function assignments and the development of metabolic models, which include pathways and enzymes (registration required).
WWW Promoter Scan.
WWW READSEQ Sequence Conversion, converts input DNA/AA sequence to specified format (input format is determined automatically), Bioinformatics and Molecular Analysis section (BIMAS), allows to convert sequences from and to 15 different formats.
WWW Signal Scan.