BME 110: Computational Biology Tools


Links & Resources

(updated throughout quarter)

Major Sequence Databases/Bioinformatics Sites
NCBI (National Center for Biotechnology Information)
GenBank, RefSeq, PubMed, Taxonomy, BLAST, and lots more
Joint Genome Institute (A leading microbial and environmental sequencing center, run by Dept. of Energy)
IMG (Integrated Microbial Genomes) - main database run by JGI, excellent genomics resource

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)
J.Craig Venter Institute (formerly TIGR, The Institute for Genome Research)
Major sequencing center, strength in microbial genome analysis (CMR), metagenome sequencing, and bioinformatics tool development

Organism-specific Databases
Human & other vertebrate genome browsers at UCSC
Archaeal Genome Browsers (Lowe Lab)
SGD (Saccharomyces Genome Database)
FlyBase (Drosophila Genome Database)

Protein Structure Databases

  • Protein Data Bank (PDB) 
  • Cath
  • SCOP
  • SWISS-MODEL
  • ModBase
  • 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

    Bioinformatics Tools Links

    EMBOSS Suite at Pasteur Institute (Mobyle interface)

    The Biology Workbench @ SDSC (slightly dated but useful, web interface)

    Genome Analysis and Interactive Annotation

    Artemis (a tool of choice for creating or updating annotation for genomes)

    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