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BME 110: Computational Biology Tools

Links & Resources

(updated throughout quarter)

Bioinformatics Tools Links

The Biology Workbench @ SDSC
The Genome Workbench @ NCBI (downloaded tool)

Protein Gene Detection

Multiple Sequence Alignments

ClustalW at EBI

Finding Restriction Enzyme Cut Sites
    New England Biolabs Tools

PCR Primer Design
    Primer 3

Structural Biology Visualization Tools

Sample visualization of SARS s2m RNA by Bill Scott

RNA Databases & Link Lists

RNA Analysis Tools

Phylogeny Tools

Major Sequence Databases/Bioinformatics Sites

NCBI (National Center for Biotechnology Information)
GenBank, RefSeq, Pubmed, nr, OMIM, BLAST, MMDB, and lots more
EBI (European Bioinformatics Institute)

ExPASy (Expert Protein Analysis System)
SwissProt, TrEMBL, ProSite
Genome Browsers at UC Santa Cruz
Many model organism genome browsers, including the Human Genome Browser
Major European genome browser site (including Human Genome)
TIGR (The Institute for Genome Research)
Major sequencing center, strength in microbial genome analysis (CMR) and bioinformatics tool development

Protein Structure Databases

  • Protein Data Bank (PDB) 
  • Cath
  • SCOP
  • ModBase

  • Organism-specific Databases

    SGD (Saccharomyces Genome Database)
    FlyBase (Drosophila Genome Database)
    Archaea Genome Browsers (Lowe Lab)

    Useful Link Pages
    UCSC Library Bioinformatics
    Links to electronic journals, databases, software, and more; information on the proxy server SlugLink for remote access to UCSC-specific resources.
    NAR Database List
    Categorized list of bioinformatics databases described in the annual NAR databases issue (January)
    Genome On-line (GOLD)
    Comprehensive listing of finished and in-progress genomes