Resources

SEQUENCE ANALYSIS SERVERS AND DATABASES

BLAST – Choose from a variety of programs for comparing DNA or protein sequences to NCBI databases
COGnitor – Search for Clusters of Orthologous Groups (COGS) of proteins in a complete genome
DDBJ - DNA Data Bank of Japan
EcoCyc - Search the genome and biochemical pathways of E. coli
ExPASy Molecular Biology Server - Compare proteins to a variety of databases
KEGG - The Kyoto Encyclopedia of Genes and Genomes
MetaCyc - A general biochemical pathway database
PDB - Protein Data Bank
PIR - Protein Information Resource
Pfam - Compare a protein sequence to multiple alignments and Hidden Markov Models
Profile Scan (Motif Scan) - Search for motifs in a sequence using Prosite and Pfam
Prosite - Search the ExPASy database of protein families and domains
PSORT - Prediction of protein localization sites in amino acid sequences
SignalP - Search for signal peptide cleavage sites in protein sequences
Tandem Repeat Finder - Locate tandem repeats in a FASTAsequence
TMHMM - Prediction of transmembrane helices in proteins
Primer3 - Pick primers from a DNA sequence

GENOME CENTERS

ACGT - Bruce Roe’s Advanced Center for Genome Technology at the University of Oklahoma Norman campus
CSHL - Cold Spring Harbor Laboratory in Cold Spring Harbor, NY
EBI - European Bioinformatics Institute in Cambridge, UK
LANL - Los Alamos National Laboratory in Los Alamos, NM
NCBI - National Center for Biotechnology Information
Sanger Centre - The Wellcome Trust Sanger Institute in Cambridge, UK
Stein Laboratory - Lincoln Stein’s lab at CSHL
JCVI - The Institute for Genomic Research in Rockville, MD
GSC - Washington University Genome Sequencing Center in St. Louis

SOFTWARE

WinImp - Free data compression/extraction software
Artemis - DNA sequence viewer and annotation tool
Phred/Phrap/Consed - A base-caller, assembler, and graphical editor
JCVI Software - Various tools for analysis of eukaryotic and prokaryotic organisms
Sanger Software - A large collection of sequence analysis Software

OTHER RESOURCES

HLA Ligand/Motif Online Database system - Under the direction of Dr. William Hildebrand, Ph.D.
CCDC - Cambridge Crystallographic Data Centre
OU Cancer Center - an information resource for Cancer Center members (who are located at OUHSC, OU Norman, OU Tulsa, OMRF, and OSU) and the public.