Online resources for the class

• Text Editors

  • TextPad (free evaluation, $29 license)

  • jEdit (free)

  • XEmacs (free, GNU)

  • Scintilla (free)

• Perl introduction and tutorials

  • Getting started with perl

  • Language basics (Perl in a Nutshell, chapter 4)

  • Perl Cookbook (Tom Christiansen & Nathan Torkington)

  • The site for people learning perl

  • Picking Up Perl

  • www.cpan.org

• Perl

  • ActivePerl

    • Web page and download area

  • O'Reilly Perl

    • Web page

  • MacPerl

    • Web page

• IDE's

  • Open Perl IDE

    • Web page and download area

    • User manual

  • Komodo ($29.95 student license)

    • Web page

• Molecular biology

  • Roche Genetics Education Program

    • Web page and online movie

  • An online review of molecular biology

  • MIT's Biology Hypertextbook is an online molecular biology textbook

  • The Cartoon Guide to Genetics, by Larry Gonick & Mark Wheelis

• Molecular biology databases
  • NAR annual compilation of Molecular Biology Databases
  • National Center for Biotechnology Information (NCBI) and specific NCBI sites:
    • Educational resources especially the Entrez tutorial
    • Entrez
    • Entrez Gene (replacing LocusLink)
    • PubMed
  • The Gene Ontology
  • Human Genome Browser Gateway Santa Cruz genome browser
  • SwissProt (US mirror) and UniProt

  • PDB

  • Stanford Microarray Datebase (SMD)

• Multiple sequence alignment (MSA)  
  • BLAST basic local alignment search tool
  • ClustalW progressive MSA program
  • BioEdit sequence alignment editor
  • DCA Divide and Conquer MSA
  • DALIGN block based MSA
  • Tmsa, IBM's pattern discovery tools
  • MAVID, multiple alignment of large genomic regions
  • A uniform interface to various MSA programs
  • Another uniform interface to various MSA programs
  • Pfam: Protein Family database of MSAs of homologous proteins
  • TigerFam: Protein Family database of MSAs based on shared function in addition to homology
  • The statistics of sequence similarity scores (NCBI)
• Phylogenetic analysis
  • PHYLIP a free package of programs for inferring phylogenies by Joe Felsenstein
  • PAUP a popular software package for inference of evolutionary trees
• Hidden Markov Models
  • SAM, an HMM creation tool, with documentation, a web server, and a download page
  • HMMer, a similar HMM creation tool
  • Pfam A protein family database built with HMMs
• Protein Structure and its Prediction
  • Critical Assessment of techniques for protein Structure Prediction (CASP)
  • Protein fold class databases: SCOP, CATH, FSSP and Homestrad
  • NCBI's Domain Guess by Size
  • Bioinfo.PL, Polish metaserver
  • Baker Lab (Rosetta) home page, the Robetta (Robot Rosetta) prediction server and the I-sites Library
  • SAM T02, T99, a HMM for homology-based structure prediction
  • Protein threading programs, TOPITS and GenThreader
  • The Amber Molecular Simulation Programs, including energy minimization and molecular dynamics
  • The Charmm A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
  • Computational Center for MacroMolecular Structures (CCMS)
  • AutoDock (Free for academic use)
  • DOCK (free for academic use)
  • 3D-DOCK suite (FTDock, RPScore and MultiDock) aimed at protein-protein interactions. Open source.
• Microarray gene expression
  • Affymetrix (GeneChips)
  • SiliconGenetics (GeneSpring)
  • HCNetDat (DNA microarray gene annotation database)
  • GO (GeneOntology)
  • GO slims (GeneOntology Slims)

   

General bioinformatics sites

• International Society for Computational Biology

• IEEE/ACM Transactions on Computational Biology and Bioinformatics

• Bioinformatics (journal)

• Journal of Computational Biology

• Journal of Bioinformatics and Computational Biology

• Pacific Symposium on Biocomputing

• Intelligent Systems for Molecular Biology (ISMB) conference

• Computational Systems Bioinformatics (CSB) conference

• Virtual Conferences and Seminars on Genomics and Bioinformatics

• Midwest Ecology and Evolution Conference (MEEC)

• Midwest Artificial Intelligence and Cognitive Science Conference (MAICSC)

• Center for Computational Genomics at CWRU

• Ohio Supercomputer Center Bioinformatics Resources

• BioInterprise Corp

Other online resources

• Online Lectures on Bioinformatics (Martin Vingron)

• Gnuplot

• Probability and statistics

  • HyperStat Online Textbook

  • Electronic Textbook StatSoft

• List of bioinformatics algorithms (maintained by Andrew C.R. Martin)

• Bioinformatics resources on the web (maintained by Zhiping Weng)

Jobs

• Bioinformatics Jobs