Web Sites
The initial set of Web sites listed is borrowed from the Trends Guide to Bioinformatics(© 1998 Elsevier Science), which was used in one of the earliest UCSC classes on bioinformatics. The headings follow those in the trends guide.
The list will grow and develop as users provide new URLs; please see the members' contributions section.
At the end is a list of education sites, thanks to the recent open day at the Stanford Genome Technology Center.
Major headings
Text based searches.
Practical searching
Computational genefinding
Multiple alignment
Protein Classification
Phylogenetics
Biological databases
Functional Genomics
Education sites
Other sites
Text based searches.
NCBI - Entrez search and retrieval system
NCBI - Entrez Help
EBI - European Bioinformatics Institute
DBGET - GenomeNet, Japan links to other databases
DBGET help
Practical searching
BLAST web site. sequence similarity
BLAST ftp site
FASTA web site sequence alignment
FASTA ftp site
Sequence and structure search site
Computational genefinding
Bibliographies
Biblio functional analysis of nucleotide sequences
More contigs from the Sanger Center
Genie (HMM) gene identification tool
GenScan (HMM)
HMMgene prediction of vertebarate and c.elegans genes
GeneMark HMM
Veil HMM
AAT analysis and annotation tool
FGENEH
GeneParser
Glimmer
Grail Oak Ridge Computational Biology
MZSF exon prediction
Procrustes spliced alignment
Multiple alignment
BLAST 2.0 server
WUBLAST Washington Univ., St. Louis
CLUSTALW
CLUSTALX
HMMER profile HMM for sequence analysis
PSI-BLAST protein database searching
Sanger Wormpep 13
SWISS PROT annotated protein sequence database
SAM sequence alignment and modeling DNA searches
HMMpro
GENEWISE
PROBE FTP directory
METAMEME
BLOCKS Fred Hutchinon Cancer Research Center, Seattle
WashU IBC multiple sequence alignment
EBI BioCatalog
Protein Classification
PROSITE home page protein families and domains
PROSITE pattern scan
PROSITE profile scan
PROSITE frame-tolerant profile scan
Pfam home page; protein families database of alignments and HMMs
SMART home page
BLOCKS home page" Fred Hutchinon Cancer Research Center, Seattle
PRINTS home page
ProDom home page protein domain database
Ortholog detection and advanced BLAST2
Phylogenetics
PAUP phylogenetic analysis using parsimony
GCG package Genetics computer group - nucleic acid and protein analysis
PHYLIP phylogenetics inference package
Hennig
MEGA/METREE Institute of Molecular Evolutionary Genetics
GAMBIT
MacClade
Biological databases
PIR superfamily protein information resource
SCOP (3D folding) structural classification of proteins
CATH (3D folding) protein structure classification - Biomolecular Structure & Modeling Unit, UCL
TRANSFAC transcription factor database
GCRDb
PKR protein kinase resource
Proweb protein family documentation
KEGG Kyoto Encyclopedia of genes and genomes
LIGAND Database for enzymed, compounds, & reactions.
EcoCyc DoubleTwist e.coli
UM-BBD
COG
MBGD
NCBI Taxonomy
Tree of life
OMIM
HGMD - human gene mutation database
Functional Genomics
cDNA array technology; the old micro array home page
Gene expression arrays
GeneFilters (Research Genetics)
Gene Discovery Arrays (Genome Systems)
Atlas™ Arrays (CLONTECH) molecular and cell biology products.
Education sites
The National Health Museum.
PBS - A question of genes.
BABEC Bay Area Biotechnology Education Consortium.
CityLab Boston University School of Medicine.
Exploratorium. Diving into the Gene Pool.
The DNA files
DNA Learning Center Cold Spring Harbor.
LBL Human Genome Program.
Natural History of Genes
RISE Resources for Involving Scientists in Education.
Other sites
Flybase a database of the drosophila genome.