Online resources and papers

Contributed units to Current Protocols series

• Basic Protein Sequence Analysis, Current Protocols in Molecular Biology (invited unit). This pre-print is a resource for you to use in a variety of projects, giving explicit "how-to" instructions on using a number of resources and interpreting their results.
  
• Phylogenomic inference of protein molecul ar function, Current Protocols in Bioinformatics (invited unit). This pre-print gives you a guided tutorial of how to perform phylogenomic inference, from gathering homologs and alignment to identifying functional subfamilies.

Core Bioinformatics Tutorials

• BLAST tutorial at NCBI. Highly recommended!
• Uppsala University course on Molecular Bioinformatics . This includes Per Kraulis' excellent slides on many algorithms in bioinformatics, including dynamic programming, ClustalW, etc.

Guides/tutorials written by members of our group for this class

• Mark Grant's guide to PFAM .
• Mark Grant's guide to BLAST.
• Using the BLAST and SAM HMM software command-line interface on the Berkeley DECF machines.

Protein structure analysis

• PDB Report dtabase, from the What-If group in the Netherlands.
• A PDF file with detailed explanation of how to evaluate a PDB structure's accuracy

Help with Unix

• UNIX help for users at the University of Edinburgh.
  

More biology background