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
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)
- Comprehensive listing of finished and in-progress
genomes