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
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