Some Useful Links

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    To make the most of your time at our course, please read carefully the following materials.
    The links below will provide you with some basic and advanced knowledge of UNIX, perl, general Molecular Biology, genomes, Bioinformatics algorithms,...

    It is strongly recommended that you update your knowledge if you are not familiar with these topics.

    Previous Courses

  • Bioinformatics and Comparative Genomes Analyses (Programmes: 2005 - 2013, with links to corresponding presentations)

    On Sequences, Genomes and Computational Methods

  • Sequence - Evolution - Function: Computational Approach in Comparative Genomics

  • Learning the Shell
  • Unix - perl
  • Bioinformatics: Writing Software for Genome Research
  • How To Look Like A UNIX Guru
  • UNIX Tools
  • Quick reference to perl syntax
  • Perl's Frequently Asked Questions

  • Primer on Molecular Biology (ppt) - Primer on Molecular Biology (pdf)
  • bioalgorithms

    Algorithms with applications in Bioinformatics

  • Suffix tree in Computational BBiology
  • Dynamic programming for sequence and stucture comparison and searching
  • Dynamic Programming
  • Dynamic Programming (wikipedia)
  • Expectation-maximisation algorithm
  • Hidden Markov Models (HMM)

    Genome Databases

  • Genome definition (wikipedia)
  • Complete Bacterial Genomes
  • Eukaryotic Genome Projects
  • Databse Of Genome Sizes
  • ncbi: Entrez Genome Project
  • TIGR: Genome Projects
  • Rat Genome Database
  • Stanford Genomic Resources
  • Genolevures
  • BROAD Institut


  • ONE for All: The Next Step for PLoS
  • PLoS Computational Biology
  • PLoS Biology
  • PLoS Genetics
  • Genome Research
  • BioMed Central

  • The R Project for Statistical Computing


  • BLAST documents
  • Program Parameters for blastall
  • BLAST Sequence Analysis Tool
  • HMM

    Multiple alignment

  • Multiple alignment algorithms
  • Types of Multiple Alignment Methods
  • Whole genome alignment
  • Whole Genome Alignment paper


  • Finding Regulatory Signals in Genomes
  • Sequence motif


  • Phylogenetics: just methods
  • Phylogenetic methods
  • The Tree of Life
  • Last universal ancestor
  • List of commented phylogenetic programs

    Molecular Evolution

  • PAML
  • Being positive about selection


  • The quest For Orthologs: finding the corresponding gene across genomes
  • Large-Scale Assignment of orthology: back to phylogenetics
  • The COG database
  • Protein families and TRIBES in genome sequence space
  • MCL - a cluster algorithm for graphs


  • CIRCOS Visualizing:Alignments, conservation, intra and inter-chromosomal relationships

    Gene Prediction

  • Gene Prediction: Similarity-Based Approaches

    Ensembl Genome Browser

  • Ensembl Genome Browser

    Writing research papers

  • How to write a research paper
  • Ten simple Rules for Getting Published
  • Ten Simple Rules for Reviewers
  • Effective steps in writing scientific papers
  • Ten Simple Rules for Selecting a Postdoctoral Position

  • Writing effective e-mail: Top 10 Tips

    Search for Citations

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  • ISI web Knowledge

    Course home page

    Fredj Tekaia