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

Microbial Genomes

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