BME 110: Computational Biology Tools


Links & Resources

(updated throughout quarter)

Bioinformatics Tools Links

The Biology Workbench @ SDSC

Sequence Conversion
    ReadSeq at Baylor Genome Sequencing Center

Protein Gene Detection


Multiple Sequence Alignments

ClustalW at EBI
Jalview

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
Uniprot
Genome Browsers at UC Santa Cruz
Many model organism genome browsers, including the Human Genome Browser
Ensembl
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
  • SWISS-MODEL
  • 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)
    Genomes On-line (GOLD)
    Comprehensive listing of finished and in-progress genomes