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

MALARIA DATABASE

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

TIM BARRELs in PDB

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

Fold-recognition at UCLA-DOE STRUCTURE PREDICTION SERVER

Sequence and Structural Similarity Searches

 

Sequence similarity searches Multi search page at EBI,

NCBI : BLAST Notebook

BLITZ ULTRA Fast Search at EMBL

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

list of GENOME SEQUENCING PROJECTS

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

Barton Group Software ALSCRIPT, AMPS, AMAS, STAMP, ASSP and SCANPS

Cohen group SoftwareBackbone-dependent rotamer library, BLoop, QPack, FOLD, Match,

Rasmol Script documentation & software

MolScript v2.0.1, Per Kraulis, Avatar Software AB

WHAT IF

HMMER Hidden Markov models of protein and DNA consensus

Biosym Insight and Discover

clustalw

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

 

Embryology

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

ANSAF

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

Journals

 

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

SCIENCE On-Line

http://www.prosci.uci.edu/

Protein Science Gopher at UC Irvine

BioMedNet

Keith Robinson Collection

Pedro's Journal page

BYTE Magazine

Elsevier

InScight, Daily Science news

 

Newsgroups

BIOSCI/bionet Electronic Newsgroup Network for Biology

bionet.announce

bionet.biology.computational

bionet.biophysics

bionet.cellbiol

bionet.general

bionet.info-theory

bionet.microbiology

bionet.molbio.bio-matrix

bionet.molbio.embldatabank

bionet.molbio.evolution

bionet.molbio.genbank

bionet.molbio.proteins

bionet.software

bionet.software.www

comp.ai.alife

sci.bio.conservation

sci.bio.evolution

sci.bio.microbiology

sci.bio.misc

sci.bio.systematics

CELL-BIOLOGY

IMMUNOLOGY

NEUROSCIENCE

WWW related

 

Networking/WWW

All About LaTeX2HTML

Welcome to Netscape

Danish

 

Danish Information Servers

Forskningsrådene - Opslag SNF

UNI-Cs

UNIX Public Domain Distribution

Centre for Crystallographic Studies in Copenhagen

Ingeniøren/net

Chaos Group at DTU

Københavns Universitet

Laboratory for Infectious Diseases

Abstracts

 

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)

Lists

 

The World-Wide Web Virtual Library: Journals, Conferences, and Current Awareness Services (Biosciences)

BUBL Information Service Web Server

Electronic Journals and Periodicals

Libraries

 

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

 

Yahoo

Excite

Webcrawler

Collected from web by;

Harpreet Singh
Junior Research Fellow
Department of Computational Biology
Indraprastha Institute of Information Technology,
Sector 39 A,New Delhi-160019.
INDIA.
E-mail: hsingh@imtech.res.in

Last update: 31/03/2001.
 
 

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