Bioinformatics

So this is the introduction to the 'dry bench', doing experiments and developing hypothesis.

Getting Data

• Genes and Proteins from Genbank
• Using BLAST to find homologues
• Setting up local Blast
• Protein 3D Structures - the pdb database.
• Finding Whole Genomes
• Finding Microarray data
• BioNumbers - the database of useful biological numbers
• Macromolecular movements - database

Analyzing Data

• Multiple Sequence alignments, especially ClustalX.
• READSEQ - cleaning up DNA sequence formatting (i.e. remove numbers)
• Looking at Protein Structres, especially with PyMOL.
• Protein Alignments
• BioCyc Pathways tools
• Cytoscape -  working with and visualizing network data
• Gemoda - unix/linux based system for finding motifs in a genetic sequence. (ie. identify motifs in promoters.
• ExPASy - many programs for analysis of protein sequences and structures as well as 2-D PAGE

Examples and Tutorials

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