COM3113 -- Fundamentals of Programming

College of Computer Science -- Northeastern University -- Fall Quarter 2001

Bioinformatics Resources

These links were developed building on the large number of links listed in Genetics Databases by Martin Bishop (Academic Press, 1999). And of course, I (RPF) used www.google.com extensively. We welcome further suggestions (jshan@ccs.neu.edu futrelle@ccs.neu.edu) from any users of these pages as to additional or alternative items to add to the list.

• Bioexplorer (rather eclectic, not exhaustive).
• Links at Doug Brutlag's lab at Stanford.
• A Canadian Lab's collection
• The WWW Virtual Library of Cell Biology (at Harvard)
• Yahoo's Biology resources

• Genbank
• EMBL

Genomes:

• Human genome project
• NHGRI (human)
• Mouse
• Arabidopsis

DNA composition, codons:

• Codon usage database.
• Codon frequency tables

DNA and related tools:

• Weizmann Institute Bio-Tools
• Tools list from the Arabidopsis project.

Proteins:

• Structural Classification of Proteins (SCOP)
• Proteins: Biogenesis to Degradation from the The WWW Virtual Library of Cell Biology.
• The proteome is more complex than the genome (Proteome Sciences) and (Proteome, Inc.)
• Hydrophobicity scales
• Amino acid substitution matrices: BLOSUM62 and PAM

Java biology-related links:

• Some biology applets.
• BioWidgets
• More on BioWidgets.
• Java-based Molecular Biology Work Bench (a bit dated?)
• Alan Robinson, an active worker in bioinformatics, visualization software, Java, etc.
• Links to bio data visualization resources.

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