General Information:

• Biocomputing Tutorials from EMBnet.
• Bioinformatics in the 21st century  
• Books on bioinformatics
• European Molecular Biology Network
• Introduction to Bioinformatics
• Introduction to sequence comparison, Keith Robison.
• Primer on Molecular Genetics, including glossary.
• Protein Sequence Alignment and Database Scanning, Geoff Barton
• Recipe book for molecular sequence analysis (ANGIS).
• Biocomputing for everyone, from the VSNS (includes Biocomputing in a nutshell).
• BioComputing WWW course at the VSNS Virtual School of Natural Sciences
• Principles of protein structure WWW course. 

Bioinformatics Databases:

• Bibliographic:
  • SeqAnalRef, sequence analysis bibliography, Expasy.
  • BIOBOB, Biocomputing biliography.
• Software:
  • The BioCatalog
  • Yellow BAGI
  • Archives for Biological Software and Databases Around the World.
  • MolBiology Software, List of software for molecular biology.
• Multi-databases browsers:
  • ACNUC.
  • SRSWWW (Oslo)
  • NIH GenoBase.
• Protein sequences:
  • SWISS-PROT.
  • OWL.
  • PIR.
  • Sagittarius PIR (announcement).
• Protein structures:
  • SCOP.
  • Protein Data Bank (PDB).
• Nucleotide sequences:
  • EMBL, EBI.
  • GenBank, NCBI.
  • DDBJ, Japan.
• Transcription factors:
  • TRANSFAC
• Patterns/families:
  • PROSITE
  • Pfam
  • PRODOM.
  • BLOCKS.
  • PRINTS.
  • Domo.
  • ProtFam (MIPS homepage).
  • SBASE, Segment BASE.
  • PROCLASS
• Structure based classifications:
  • Tree classification of PDB (by Alexandrov and Fischer using SARF2).
  • CATH Protein Structure Classification
  • SCOP Structural Classification of Proteins.
  • PDB chain clustering produced by Fischer et al.
• Misc.:
  • FlyBase
  • GeneCards
• Lists of databases:
  • LiMB (gopher).
  • BioDatabases List.
• Longer list

Bioinformatics Sites:

• ANGIS Australian National Genomic Information Service.
• ANU Bioinformatics Hypermedia Service.
• B3E, Bioinformatics in France.
• BIBISERV, Bielefeld University Bioinforrmatics Server.
• Bioinformation Systems
• BioMOO The Virtual Meeting Place for Biologists
• BioBox, Finland.
• Bioexchange.com
• Bioinformatics and Computational Biology at George Mason University.
• BIOSCI, Bionet electronic newsgroups.
• BSM, Biomolecular Structure and Modelling at UCL.
• CBS, Center for Biological Sequence Analysis, Technical University of Denmark.
• Centre of Bioinformatics, Peking.
• CGATBSS, Canadian Genome Analysis & Technology (CGAT) Bioinformatics Support Services.
• Computational Biology USC, University of Southern California
• DDBJ DNA data bank, Japan.
• DoubleTwist
• EMBnet node in Oslo.
• EBI, the EMBL Outstation Hinxton.
• EMBL, Heidelberg.
• EMBnet, the European network for molecular biology.
• Expasy, Geneve.
• GDB Genome Data Base.
• HUJI, Hebrew University of Jerusalem Hadassah Medical School: The Genomic and BioInformatics Server.
• HUM-MOLGEN Human Molecular Genetics.
• Human Genome Project Information
• Information theory and molecular biology, Tom Schneider's group.
• ISREC (Swiss Institute for Experimental Cancer Research), Bioinformatics Group.
• The Johns Hopkins University BioInformatics Web Server.
• NCBI National Center for Biotechnology Information (USA).
• NLM National Library of Medicine (USA).
• Nee-How, The Bioresource Finder
• Sanger centre, Hinxton, England.
• SEQNET, Daresbury, England.
• UCSC Computational Biology
• UK MRC HGMPRC UK Human Genome Mapping Project Resource Centre.
• W. M. Keck Center for advanced training in computational biology.
• WWW in Biology, bionet.software.www.

Programms and Tools:

• Biochemical networks 
• Biosequence structure searching program 
• Clustal W, multiple sequence alignment
• GCG, Wisconsin Sequence Analysis Package Program Manual
• Genome Channel
• J-Express, a tool for analysing microarray gene expression data
• MEME, Multiple EM for Motif Elicitation
• MolScript, program for creating molecular graphics in the form of PostScript plot files
• PairWise and SearchWise, Ewan Birney's excellent tools for sequence alignment and search.
• Phylip, phylogenetic analysis.
• Pratt, pattern discovery.
• PROPHET, UNIX based software package for data analysis
• Protein topology pattern discovery (learning) program
• Protein topology pattern discovery (learning) program with visualisation 
• Protein topology searching program
• RasMol, free program which displays molecular structures
• Space Explorer: Interactive Visualisation of Relationships between Objects 
• Topology-based protein structure comparison program
• Visualising relationships in protein topology space

Services Online:

• AMAS Analysis of multiple alignments (Geoff Barton).
• BCM Search Launcher searches, alignments.
• Bioinformation Search Center
• Biologist's Control Panel (Baylor college of medicine).
• Block Maker, at Fred Hutchinson Cancer Research Center.
• Database searches, EBI (Fasta, Blitz,...).
• Database searches at DISC (Japan) -- includes Fasta, BLAST, MPsrch and SRS Fasta
• Expression Profiler - online tool for expression profile clustering and sequence pattern discovery
• ExPASY Molecular Biology Serever
• Longer list
• Match sequence against PROSITE.
• MEME, motif discovery tool.
• MSA, Clustal W multiple sequence alignment
• Pratt - pattern discovery online
• PredictProtein , Heidelberg.
• PSA, Protein Sequence Analysis: fits a structure model to your sequence.
• SAM, Sequence alignment and modeling system (using HMMs).
• Sequence analysis tools, PDB, including multiple sequence alignment.

Courses Online:

• Algorithms for Molecular Biology - Course Homepage , Israel.
• Bill Pearson on homology search.
• Bioinformatics course in Bergen.
• Bioinformatics by Dr. Schaefer
• Bioinformatics courses at George Mason University.
• Biocomputing Course Resource List
• Computational Biology Course, Hopkins
• Computational Molecular Biology at Washington University.
• Dirichlet mixtures, improving detection of weak homologies.
• How to become a bioinformatics expert, list of European courses.
• International Master's programmein Bioinformatics at Chalmers University of Technology, Gothenburg, Sweden.
• Keck Center, Pittsburgh, Pennsylvania.
• Medical informatics, Pittsburgh, Pennsylvania.
• Medical Information Sciences 214 - Representations and Algorithms for Computational Molecular Biology, Stanford.
• PSB Biocomputing Education workshop
• Regularizers for estimating amino-acid distributions.
• SAM, Sequence alignment and modeling system (using HMMs).
• The Penn Computational Biology Training Program.
• Tutorials and Lecture Notes on Bioinformatics 
• University Bioinformatics Programs - list provided by IHCP
• VSNS Multiple Alignment Resource Page

Journals Online:

• Bioinform
• Bioinformatics 
• Bioinformatics Online
• CABIOS
• Genome Research
• IDEAL, International Digital Electronic Access Library - online abstracts. 
• In Silico Biology, online journal
• Journal of Computational Biology
• Journal of Molecular Biology.
• Nature
• Nature, Genome Gateway
• Nucleic Acids Research (NAR)
• Proceedings of the National Academy of Sciences of the United States of America (PNAS) 
• Protein Science.
• Proteins: Structure, Function and Genetics
• PubMed, database of journals.
• Science Online
• The Bioinformer, published by EBI.

Other Links:

• Amos' WWW links.
• BioInformatics forum in Bergen
• Biolinks from Bioplanet
• Biologists's Control Panel includes searches of many databases.
• Biotechnology Software, maintained by The National Biotechnology Information Facility
• Bio-wURLd.
• BRASS, Bioinformatics Resource for Algorithms, Software and Sequences.
• CBPE, Center for Biotechnology Policy and Ethics.
• DNA Computers, by Yali Friedman.
• ELSI, Ethical, legal and social implications of biotechnology.
• Eubios Ethics Institute
• International Society for Bioinformatics
• Is a genome like a computer program, Gary Welz.
• List at SEQNET
• International Society for Computational Biology
• Jeff's biolinks, Yale University.
• Laboratory of Computational Genomics
• Motif Bioinformatics Server, Stanford.
• Nee-How, The Bioresource Finder
• Pasteur Institute.
• Pedro's BioMolecular Research Tool.
• PhD thesis on DNA computers
• Search engine biological Web Sites.
• Showcase for new WWW servers.
• Society for Bioinformatics in the Nordic Countries
• Survey of Molecular Biology Databases and Servers, R. Smith.
• The Bioethics Internet Project,
• The DNA files, WWW pages of US radio program series on Human Genome research and its applications.
• The Molecular Biologist's Desk Reference.
• The World-Wide Web Virtual Library: Biosciences, Harvard.
• Web Resources for Protein Scientists, Protein Science.