ABIM Guide de logiciels

     Guide d'utilisation de logiciels - Cours

English version

Quelques guides, en ligne, d'utilisation de logiciels

Accès à des banques - Soumission
- Description des banques EBI (UK)
- DBCAT (The Public Catalog of Databases) InfoBioGen
- The DDBJ/EMBL/GenBank Feature Table Definition EBI (UK), voir aussi NCBI (USA)
- ACEDB Documentation AceDB
- EMBL Documentation EBI (UK)
- Genbank Overview NCBI (USA)
- Genbank : description des fichiers (NCBI)
- PDB Documentation and Information RCSB (USA)
- PIR Information Ressources Georgetown (USA)
- SRS 5 Help Heidelberg (Une description résumée de chaque banque accessible sur un serveur SRS 5 est donnée, voir "Data Banks de la page séquence)
- SRS 6 Manual InfoBioGen
- SRS 7 Manual InfoBioGen
- SWISS-PROT (et UniProt) Documentation EBI (UK)
- SWISS-PROT Protein Sequence Database (et UniProt) documentation
- SEQUIN NCBI
Alignement sur une banque
- BAliBASE: A benchmark alignments database for the evaluation of multiple sequence alignment programs Strasbourg (France)
- Beauty-X BCM (USA)
- BLAST Man NCBI
- BLAST Course (Altschul) NCBI (USA)
- BLAST FAQ NCBI
- BLAST Overview NCBI
- BLAST Tutorial NCBI
- BLAST tutorial Pasteur
- BLITZ (BIC) Server Documentation Shane Sturrock and John Collins, voir MPsrch
- NCBI Education NCBI
- Profile documents ISREC
- Protein Sequence Alignment and Database Scanning Geoffrey Barton (article général)
- Biosequence comparison Keith Robison (article général)
- SCANPS Geoffrey Barton
Alignements de séquences
- AMAS EBI
- ClustalW On-line Help, ou encore NIH
- MSA manual ou NCBI
- Pattern Matching Pointers (People, journals, software) Purdue (USA)
- SAM (Sequence Alignment and Modeling) UCSC (USA)
- Seqaln Pasteur
Motifs ..
- Aide pour écrire des expressions régulières en Perl ABIM (utilisation de PatternFind)
- Pattern Matching Pointers (People, journals, software) Purdue (USA)
- Prosite Sever Documentation Expasy
- Protein Motif Fingerprint Database Manchester
- User's Guide for HMMER Protein and DNA Hidden Markov Models Washington, autre lien
Phylogénie
- ClustalW 1.7 Strasbourg
- Computer Intensive Methods in Phylogeny Stanford (USA)
- Hennig86 Cladistics
- LVB manual Pasteur, en fichier pdf
Structure
- MC-SYM user's guide (Montréal)
- CCP4 Program (cristallography)
- RasMol open-Rasmol, voir aussi Berkeley
- THREADER (London) www : predicting protein tertiary structure by recognizing the correct fold from a library of alternatives
- VMD tutorial Illinois (USA)
- WHAT IF CMBI
- X-PLOR Yale (Axel Brunger's Research Group)
- Zuker's Mfold (RNA) manual
Ensemble de programmes
- GCG NIH, voir aussi "GCG beginner's FAQ"
- Gene-finding and machine learning systems (Pirate, Twain, Glimmer, MUMer, ...) Maryland (USA)
- GRAIL et GrailEXP ORNL
- PISE (a tool to generate Web interfaces for Molecular Biology programs) Pasteur
- PHYLIP (Phylogeny Inference Package) InfoBioGen, ou encore Joe Felsenstein (Washington)
- Phylip, Lamarc, PopG, DNATree Washington
- Software/Documentation Links Manchester (CCP4, X-PLOR, Raster3D, RasMol, ..)
- STADEN Software manual (Minnesota)

Cours - Divers
- 2can Bioinformatics EBI (UK)
- Algorithms for Molecular Biology Tel-Aviv (Israel)
- Algorithms in Molecular Biology (Karp, Ruzzo and Tompa) UW (fichiers pdf ou postscript)
- BASICS in BIOINFORMATICS Konstanz (Allemagne)
- BIMM 140 SDSC (USA)
- Biocomputing For Everyone Bielefeld (Allemagne)
- BioComputing Hypertext Coursebook (Pairwise Sequence Alignments, Networking, Multiple Alignment, Mathematical Basis of Molecular Phylogenetics, Genetic Algorithms and Protein Folding) BCD (Allemagne), miroir à IST (Italie)
- Biocomputing Tutorials Isrec (Suisse)
- Bioinformatics course web (BE561, BF821, BE777) Boston (USA)
- Bioinformatique (Cours et ressources) InfoBioGen (France)
- BioPerl EBI (UK)
- CSB resources guides (Data Reduction and Analysis, Molecular Graphics, Sequence Manipulation and Analysis) Yale (USA)
- Computational gene recognition bibliography Rockefeller (USA)
- CORBA (Common Object Request Broker Architecture) EBI (UK)
- CS 439 Computational Biology Course (Challenges in the Human Genome Project, A survey of sequence comparison algorithms, A New Algorithm for DNA Sequence Assembly, Hidden Markov Models in Computational Biology, Locating Protein Coding Regions in Human DNA using a Decision Tree Algorithm, A System for Induction of Oblique Decision Trees (fichiers ps)) John Hopkins (USA)
- EMBOSS tutorial EMBnet, autre lien
- The Genetic Algorithms Archive NCARAI (USA)
- Cours de Bioinformatique (Banques et recherche de similitudes) DSI (France)
- Courses on Bioinformatics Rockfeller (USA)
- Course Syllabi BCD
- Démystifier l'ordinateur en Biologie Jussieu
- Distant homologies : motifs, patterns, profiles ICGEB (Italie)
- Documentation and bioinformatics courses HGMP (UK)
- GEML (Gene Expression Markup Language) GEML (USA)
- Guide to Structure Prediction EMBL (Allemagne)
- Introduction to Computational Molecular Biology MIT (USA)
- Introduction to Human Genome Computing via W3 CSHL (USA)
- Introduction to Programming using Python Pasteur
- List of Bioinformatics courses Pekin (Chine)
- Méthodes et Algorithmes pour la Génomique Montpellier (France)
- Molecular Modelling for Beginners BMCI
- Molecular Systematics and Evolution Newcastle (UK)
- NCBI Education NCBI
- OUBC Tutorials (GCG, Staden, Phylogeny) Oxford (UK)
- Polycops InfoBio (Introduction à la bioinformatique, Prédiction de structure secondaire, Méthode NJ) ABIM (Marseille)
- Pacific Symposium on Biocomputing PSB (1996 - 2006)
- Protein Sequence Analysis : a practical guide Manchester (UK)
- Representations and Algorithms for Computational Molecular Biology Stanford (USA)
- Sequence comparison Rouen (France)
- Similarity Searching Guides and Documentation HGMP (UK)
- Software/Documentation Links Manchester (CCP4, X-PLOR, Raster3D, RasMol, ..)
- Tcl ressources Pasteur
- Tutorials on sequence analysis Columbia (USA)
- Virtual School of Natural Sciences (Alignements, Matrice de coût de substitutions, Algorithme génétique pour l'étude du repliement des protéines ...) disponibles sur plusieurs sites BCD (Allemagne), Gênes (Italie) : paragraphe : Our Online BioComputing Tutorial and Hypertext Coursebook ( voir aussi le sous-paragraphe : Examples of Hypertext Books)

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