HELP HOME MHC & Prediction Algorithms

HLA-related links

BSHI2001 Meeting..
IHW2002 Meeting..
MHC Chapter in Kuby's Immunology..
HLA Dictionary
WHO Nomenclature & HLA Sequences at the ANRI ..
Complete MHC Sequence
CD Antigens and KIR Nomenclature
Bone Marrow Donors Worldwide ..
World Marrow Donor Association
MHC Database
MHC-Peptide Database ..
IMGT/HLA Immunogenetics Database
Peptide Binding Motif Prediction Database (SYFPEITHI) ...
HLA Motif - Sequence Scanner
Human Chromosome 6 Project at the Sanger Centre ...
Genes on Chromosome 6
ECACC Online - IHW Cell Line Panel...
Jackson Lab - Mouse Strains
South Thames Tissue Typing Laboratory . .
Michigan Transplant Center
Geraghty Laboratory ...
Stanford University Population Genetics Laboratory ..
Nei's Laboratory
Potts&PennLaboratory. .
Thompson Laboratory
A Lecture on Linkage Disequilibrium ..
EH Linkage Disequilibrium Software
Constrained Disequilibrium Value Calculation
PopGene Freeware (HW equilibrium, linkage disequilibrium, genetic distance, etc)
Genetic Data Analysis (GDA) Software Download ..
GDA Course (Distance Education)
Tools for Population Genetic Analysis..
Genetic Analysis Software
Cold Spring Harbor Laboratory: DNA Learning Center
 Virtual Immunology Laboratory (Howard Hughes) ..
Cytokine Gene Polymorphisms
Immunogenetics, ImmunityandHardy-Weinbergin Encyclopedia Britannica
Histocompatibility Molecules in Kimball's Biology
Mouse Genetics by Lee Silver (full text book)
Links to Immunology, Genetics and Epidemiology Journals ...
Links to Evolution-Related Sites. .
Evolution / Genetics Glossary...
Real Time PCR
Electronic Statistics Textbook and Glossary ...
InStat Guide to Statistical Tests
Adenoviruses Fact Sheet ...
HIV Sequence Database
MHC and Sexual Selection
HLA and Leukemia  .
HLA-DR53 Fact File . .
HLA and Statistics




Bioinformatics links

Databases over Databases and Tools

SRS Sequence Retrieval System: Network Browser for Databanks in Molecular Biology
Survey of Molecular Biology Databases and Servers
The BioMedNet Library
Search facility for Databases and Resources for Computational Genetics
DBGET Database Links
Harvard Biological Laboratories - Genome Research databases and selected servers
Johns Hopkins Univ. OWL Web Server
Index of Biology Internet Servers, USGS
List of documents concerning molecular biology oriented services, software, email servers, FTP sites at ExPASy
Listing of Molecular Biology Database (LIMB)
WWW Server for Virology, UW-MADISON
UK MRC Human Genome Mapping Project Resource Centre
PEDROS (the pioneer) list of Molecular Biology Search and Analysis tools
Links to other Bio-Web servers
Molecular modelling servers and databases
Web Resources for Protein Professors
ExPASy Molecular Biology Server
The Antibody Resource Page
Bioinformatics WWW Sites
Bioinformatics and Computational Biology at George Mason University
INFOBIOGEN Catalogue of Databases
Biobase in Denmark
National Biotechnology Information Facility, New Mexico
Biological Sciences, Directory, SciCentral
Jeffs Biolinks
WWW for Crystallographers
WWW Resources for Model Organisms

Main Databases

ExPASy Molecular Biology Server
SWISSPROT protein sequences
PROSITE, functional protein sites
PROTOMAP - hierarchical classification of SWISSPROT
EMBL WWW Services
Genbank Database Query Form, get a GENBANK entry
Brookhaven Protein Data Bank WWW Server, Get a structure
website for producing lists of PDB chains with maximum mutual sequence identity ao/A>
dbEST Expressed Sequence Tags
Macromolecular Structures Database
Molecules R US Utility Search and view a proteins molecule
PIR-International Protein Sequence Database
SCOP: Root: scop, Structural Classification, MRC
HIV sequence Database, Los Alamos
HIV Molecular Immunology Database, Los Alamos
TIGR Database, Human Genome, Arabidopsis thaliana, Haemophilus influenzae, Mycoplasma genitalium
European Bioinformatics Institute (EBI), EMBL Nucleotides, SWISS-PROT Proteins
MEDLINE WWW Entrez PubMed Browser
The NCBI WWW Entrez Browser
Cambridge Structural Database, small-molecule organic and organometallic crystal structures
Protein Research Foundation, Japan: LITDB; Literature Database, SEQDB; Peptide/Protein Sequence Database
Human genome sequencing data Weizmann Links.
DNA Information and Stock Center DISC, National Institute of Agrobiological Resources, Tsukuba, Japan.

Specialized Databases

Protein Disease Database (PDD)
ANU Bioinformatics Hypermedia Server Virus databases, Classification and Nomenclature of Viruses
O-GLYCBASE A revised database of O-glycosylated proteins
The Genome Sequence Database (GSDB) Complete, publicly available relational database of DNA sequences and annotation
The metabolic pathway collection from EMP The enzymes and metabolic pathways database
Compilation of DNA sequences of Escherichia coli K12 ECDC sequence contigs, Genetic map of E.coli K12, Searchable index
The Haemophilus influenzae database collection Genetic map of H.influenzae, contigs, Searchable index
EcoCyc An encyclopedia of Escherichia coli genes and metabolism, graphical user interface
GenProtEc Genes and proteins of Escherichia coli
NRSub A non-redundant database for Bacillus subtilis
YPD A database for the proteins of Saccharomyces cerevisiae
LISTA, LISTA-HOP and LISTA-HON A comprehensive compilation of homology databases from the yeast Saccharomyces
FlyBase The Drosophila database
MPDB Molecular probe data base
tRNA sequences and sequences of tRNA genes Server der Universität Bayreuth
Small RNA database Baylor College of Medicine
The uRNA database University of Texas
SRPDB The Signal Recognition Particle Database
RDP The Ribosomal Database Project
Database on the structure of small ribosomal subunit RNA
Database on the structure of large ribosomal subunit RNA
The RNA modification database
HAMSTeRS The haemophilia A mutation search and resource, factor VIII mutation database
Haemophilia B Database of point mutations and short additions and deletions (sixth edition)
human p53, hprt and lacZ genes Databases of mutations in human p53 gene, hprt gene and lacZ gene in transgenic rodents
PAH Mutation Analysis Consortium Database disease-producing human PAH loci
ESTHER A cholinesterase genes server
IMGT The immunogenetics database
p53 mutations Database of p53 mutations in human tumors and cell lines
The androgen receptor gene mutations database
The glucocorticoid receptor resource
The Thyroid Hormone Receptor Resource
16SMDB The 16S ribosomal RNA mutation database
23SMDB The 23S Ribosomal RNA Mutation Database
MITOMAP human mitochondrial genome database
SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis
PRINTS protein fingerprint database
KabatMan Database of antibody structure and sequence information
ALIGN Compendium of Protein Sequence Alignments
CATH Protein structure classification system
protein domain database
The Blocks database a system for protein classification
HSSP The HSSP database of Homology-derived Secondary Structure of Proteins
FSSP database fold classification based on structure-structure alignment of proteins
SBASE The SBASE protein domain, a collection of annotated protein sequence segments
TransTerm A database of translational signals
GRBase A database linking information on proteins involved in gene regulation
ENZYME nomenclature of enzymes
REBASE Database of restriction enzymes and methylases
RIP The Ribonuclease P Database
TRANSFAC A database on transcription factors and their DNA binding sites
MHCPEP a database of MHC-binding peptides
The Mouse Genome Database
ATCC - American Type Culture Collection
Histone Sequence Database compilation of highly-conserved nucleoprotein sequences
3Dee A Database of Protein Structure Domain Definitions
NRL_3D sequence--structure database derived from PDB, Pictures and searches
VBASE Human Variable immunoglulin Gene Sequences
GPCRDB G protein-coupled receptor ( GPCR ) data
Other Organisms Genome Databases ACeDB-C. elegans, MycDB-Mycobacteria, PatoGenes-fungal pathogens of cereals
Mouse Knockout Database
Locus Specific Mutation Database
Carbohydrate Databases
The Human Papillomaviruses Database
Human 2-D PAGE Databases for Proteome Analysis in Health and Disease
the Kidney Development Database
The U.S. Patent Citation Database
Animal Genome Database, Japan
Database of 3D structures of lectins
HIC-Up, Hetero-compound Information Centre - Uppsala
Nucleic Acid Database (Structural)
HOVERGEN, homologous Vertebrate Genes Data Base, Release 31
Database of Macromolecular Movements
PROLYSIS dedicated to proteases and their inhibitors

Predictions of protein structure from sequence

Burkhard Rost: run the PHD PredictProtein server Secondary Structure, solvent Accesibility and transmembrane segments
PhdThreader Fold recognition by prediction-based threading
Protein Structural Analysis, BMERC. Protein Structural Analysis (under construction)
Submission form for protein domain and foldclass prediction
NNSSP Program Description Prediction of protein secondary sturcture by nearest-neighbor algorithms
Swiss-Model An Automated Knowledge-based Protein Homology Modelling Server: first attempt to a sequence to structure server
PHD secondary structure prediction by Neural Network.
SSPRED secondary structure prediction with multiple alignment
SSCP secondary structure prediction content with amino acid composition
SOPM Self Optimized Prediction Method at IBCP, France.
NNPREDICT A two-layer, feed-forward neural network for residue by residue prediction
MultPredict Predict Secondary structure based on multiple sequence alignment.
TMAP A service predicting transmembrane segments in proteins
TMpred Prediction of Transmembrane Regions and Orientation
MultPredict Prediction Secondary Structure of Multiply Aligned Sequences
NIH molecular Modelling Homepage A modelling homepage with links
BCM Search LauncherProtein Secondary Structure Prediction
COILS Prediction of Coiled Coil Regions in Proteins
Paircoil program predicts the location of coiled-coil regions in amino acid sequences.
PREDATOR Protein secondary structure prediction from single sequence
Dense Alignment Surface "DAS" prediction of transmembrane regions in proteins

Sequence and Structural Similarity Searches

Sequence similarity searches Multi search page at EBI,
NCBI : BLAST Notebook
EMBL WWW Services
BioSCAN Online at U. North Carolina
Pattern Scan of Proteins or Nucleotides, PATSCAN
The PRINTS/PROSITE Scanner Search motif databases with query sequence
BLOCKS/PRINTS scanner Search BLOCKS or PRINTS motifs databases(in blocks format)
Blast search against SBASE at ICGEB
The DARWIN system ETH zurich search Tools
PimaII This finds sequence similarity using Dynamic Programming
DashPat This finds sequence similarity using a hashcode comparision with a pattern library
PROPSEARCH Search based on amino acid composition, EMBL
A sequence search protocol A sequence search protocol, integrated pattern search
GenQuest Fasta, Blast, Smith Waterman Search in any database
SSearch Searches against a specified database
BCM Search Launcher Makes multiple searches from one input.
Peer Bork Search list Motif/Pattern/Profile searches
EBI: Sequence Data Analysis
PROSITE Database Searches, Search for functional sites in your sequnce
PROWL - Protein information On-line Retrieval WWW Lab Search with MW and peptides digest
FASTA-SWAP or FASTA-PAT Search of a Pattern Database Profile and pattern searches
CEPH Genotype database
Advanced BLAST2 Search at EMBL
ProfileScan Server, ISREC
TOP: For comparisons and similarity searching in database for 3D protein structures
Hidden Markov similarity searches at UCSC
Toplogy-based Protein Structure Comparison
The Biology WorkBench

Gene finding methods and gene, Promoter, DNA, RNA, related Links

BCM genefinder Solovyev
NetGene Intron splice sites in human genes
NetPlantGene Intron splice sites in Arabidopsis thaliana DNA
Genequiz automated analysis of genomes
BCM Search Launcher Gene Feature Searches, GRAIL and others
GRAIL version 1.3 interface Protein Coding Regions and functional sites
GENMARK WWW System for predicting protein coding regions
FGENEH Genefinder: Prediction of gene structure in human DNA sequences
GRAIL and GENQUEST E-mail Sequence Analysis, Gene Assembly And Sequence Comparison Systems
Eukaryotic Pol II Promoter Prediction
Scans DNA sequences for eukaryotic transcriptional elements
Gene discovery page
Gene-map Homology Search
Cytogenetic Correspondence in the Linkage Map
Alphabetic list of genetic analysis software
Promoter Prediction by Neural Network
Genie: A Gene Finder Based on Generalized Hidden Markov Models
Splice Site Prediction by Neural Network
Signal Scan: scans DNA sequences for eukaryotic transcriptional elements
The rRNA Database and WWW server, University of Antwerp (UIA)
RNAstructure, Turner group
Bioinformatics (Genomics)

Various Prediction and structure Servers

DictyOGlyc GlcNac O-glycosylation sites in Dictyostelium discoideum.
NetOglyc GalNac O-glycosylation sites in mammalian proteins
Signalp Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
PSORT Prediction of Protein Sorting Signals and Localization from sequence
Prediction of HLA binding peptides from sequence at BioInformatics & Molecular Analysis Section (BIMAS) by Dr. Kenneth Parker and Ronald Taylor
EpiMatrix MHC-Binding Prediction Gabriel E. Meister, Anne S. De Groot et al. at Brown University and implemented by AVX Design Inc

Sequence and structure Alignment

Pairwise Protein Alignment SIM at expasy, and LALNVIEW alignment viewer program
Pairwise DNA Alignment (LFASTA) ACNUC at Lyon
Clustal W
AMAS Analyse Multiply Aligned Sequences
BCM Search Launcher Multiple Sequence Alignments
BCM Search Launcher Pairwise Sequence Alignment
DALI Comparing protein structures in 3D
Protein Sequence Alignment and Database Scanning A review by Geoffrey J. Barton
Sequence Alignment (II): Principles, Algorithms and Parameters Bioinformatics Lecture Notes: Chapter 4
DIALIGN, aligment program not employing any kind of gap penalty!
TOP program for 3-d protein structure comparisons, G. Lu
comparison of protein topology
Hidden Markov alignment at UCSC

Multiple alignment and Phylogeny

SOME AVAILABLE PHYLOGENY PROGRAMS A compilation from the PHYLIP version 3.5 documentation.
A distributed Internet project containing information about phylogeny and biodiversity.
A list from the "The Tree of Life".
Cladistic Software A list from The International Willi Hennig Society.
Hidden Markov Multiple alignment at UCSC
Links to recombinant analysis programs

Molecular Biology Software Links

The EBI Molecular Biology Software Archive
Archives for Biological Software and Databases Around the World
Software Archives for Biology
Cohen group SoftwareBackbone-dependent rotamer library, BLoop, QPack, FOLD, Match,
Rasmol Script documentation & software
MolScript v2.0.1, Per Kraulis, Avatar Software AB
HMMER Hidden Markov models of protein and DNA consensus
Biosym Insight and Discover
DSSP program
collection of biosoftware ftp servers
Bootscanning for viral recombinations, Henry M. Jackson -Mika Salminen
Blocking Gibbs Sampling for Linkage Analysis in Very Large Pedigrees
ProMSED: Protein Multiple Sequences EDitor for Windows 3.11/95
DBWatcher, version 2.00 beta for Sun/Solaris, Frederic PLEWNIAK, IGBMC - Strasbourg, France
ProFit V1.7 - Protein Least Squares Fitting Software, Andrew C.R. Martin
Indiana University IUBIO software and data
Molecular Biology Software list at NIH (mainly genomic)
ProAnalyst PROTEIN ANALYST ver 1.02, new software for protein/peptide analysis
Learn about Molsoft, L.L.C. ICM, homology modelling, docking, folding
DRAGON protein modelling tool using Distance Geometry
Molecular Surface Package
Molecular Simulations Inc.
Ribbons: A software that interactively displays molecular models
Numerical Recipes in C online
WPDB protein structure display tool for Windows 3.1, Windows 95 and Windows NT
Uppsala Software Factory - MOLEMAN2 Manual
Protein Morpher, Eric Martz

Molecular biology protocol collections:

Molecular Biology Protocols (Northwest Fisheries Science Center)
Comprehensive Protocol Collection (Ambros Lab)
Molecular Biology, Biochemistry, and Cell Biology Protocols (David Bowtell)
Protocols for Recombinant DNA Isolation, Cloning, and Sequencing (Bruce Roe)
Whitehead Institute/MIT Center for Genome Research
Frontiers in Bioscience: Protocols
Promega Corporation Technical Resources

PCR protocols:

PCR II - A Practical Approach Mutational Analysis: New Mutations (K. Michaelides)
Boehringer Mannheim PCR Applications Manual
Laboratory Protocols List (Lazo Lab)

Electrophoresis protocols:

Molecular Biology Techniques Manual (University of Cape Town)
FMC BioProducts Technical Information
Technical Information on 2-D PAGE (ExPASy)

Cell biology protocols:

Cell Biology Laboratory Manual (William H. Heidcamp)

Antibody preparation protocols:

Antibodies from Design to Assay
Mitchison Lab Protocols

Cell culture protocols:

Bart's Cookbook and Lab Protocols (Sefton Lab)
Donis-Keller Lab Manual
Industrial In Vitro Toxicology Group

Immunocytochemical protocols:

Michael Serfas' Lab Protocols
Childs Lab Cytochemical Protocols
Histotechnology Technical Methods (University of Nottingham)
Faulkner-Jones Protocols
Spector Laboratory Protocols

Yeast protocols:

Herskowitz Lab Protocols
Yeast Transformation Home Page (Geitz Lab)
Botstein Lab Protocols
Forsburg Lab Protocols

C. elegans protocols

Jorgensen Lab Protocol Database
Comprehensive Protocol Collection (Ambros Lab)

Drosophila Melanogaster protocols:

Carthew Lab Manual

Arabidopsis Thaliana protocols:

Arabidopsis: The Complete Guide
Cold Spring Harbor Arabidopsis Molecular Genetics Course Manual - 1996
Meyerwitz Lab Protocols

General plant protocols:

Lazo Laboratory Protocols List

Xenopus Oocyte protocols:

Mitchison Lab Protocols

Mouse protocols:

Schimenti Lab Technical Protocols

Protocols discussion:

Technical Tips Online
bionet.molbio.methds-reagnts Newsgroup Archive
Paul Hengen's Methods and Reagents FAQ list
Nice online textbook on introductory molecular biology

Bioinformatic Groups and Colleages

The UCL Biomolecular Structure Group. Janet Thornton
Fred Cohen Laboratory
Oxford, Barton Group
Centre for Protein Engineering Cambridge, UK, Tim Hubbard group
EMBL, Cristian Sander Group
EMBL, Patrick Argos Group
CAME, Manfred Sippl Group
ICGEB, Sandor Pongor Group
Information Theory and Molecular Recognition Tom Schneider group
David Eisenberg Research Group
IRBM Biocomputing Unit, Anna Tramontano
The Walter & Eliza Hall Institute
Ludwig Institute for Cancer Research
Caltech Genome Research Laboratory
BioInformatics & Molecular Analysis Section (BIMAS) at NIH
MRC, Mathematical Biology: Willie Taylor group
Centre for Crystallographic studies in Denmark
C.N.R.S. Structural & Genetic Information
Weizmann Institute of Science, Genome and Bioinformatics, Israel
Gerard J. Kleywegt, Uppsala
George M. Church Laboratory, Harvard


BioInformer, a quarterly newslette
Mutation Research/DNA repairMan
ISI Impact Factors 1994
AAAS Home Page
Nature - Welcome
Nature - Structural Biology
Journal of Virology
Electronic Protein Science Home Page
Journals: Oxford Online Journals : Nucleic Acids Research Online
Electronic Journals and Periodicals
Nucleic Acids Research Online
Protein Science Gopher at UC Irvine
Keith Robinson Collection
Pedro's Journal page
BYTE Magazine
InScight, Daily Science news


BIOSCI/bionet Electronic Newsgroup Network for Biology

WWW related

All About LaTeX2HTML
Welcome to Netscape


Danish Information Servers
Forskningsrådene - Opslag SNF

UNIX Public Domain Distribution
Centre for Crystallographic Studies in Copenhagen
Chaos Group at DTU
Københavns Universitet
Laboratory for Infectious Diseases


The NCBI WWW Entrez PubMed Browser (very good)

News Conferences etc.

CNN Interactive
Welcome to Pathfinder
The World-Wide Web Virtual Library: Journals, Conferences, and Current Awareness Services (Biosciences)


The World-Wide Web Virtual Library: Journals, Conferences, and Current Awareness Services (Biosciences)
BUBL Information Service Web Server
Electronic Journals and Periodicals


online dictionary, cell biology
online dictionary, genetics
NLM HyperDOC: World-Wide Web (WWW) Server of the U.S. National Library of Medicine (NLM)
Library of Congress World Wide Web Home Page
Danmarks Natur- og Lægevidenskabelige Bibliotek
BIODIDAC Catalog Bio pictures
Encyclopedia Britannica online

General WWW Search Engines


Collected from web by;

Harpreet Singh
Junior Research Fellow
Department of Computational Biology
Indraprastha Institute of Information Technology,
Sector 39 A,New Delhi-160019.

Last update: 31/03/2001.
HELP HOME MHC & Prediction Algorithms