|
Category |
Databases
and Web Sources |
Note |
|
Web
resources |
NCBI |
|
|
|
European Bioinformatics Institute (EBI) |
|
|
|
Weizmann
Institute |
|
|
Genomics-databases
and web sites |
GenBank-Entrez
|
Sequence
and structure |
|
|
dbEST |
DNA |
|
|
UniGene |
Gene-oriented
cluster |
|
|
dbSNP |
Sequence
variation |
|
|
GDB |
Human
genome database |
|
|
Ensembl |
Annotation
on genomes |
|
|
Genome
Channel |
|
|
|
GeneLoc
(UDB) |
Human
genome mapping |
|
|
VISTA Genome Browser |
Browse
whole-genome |
|
|
Human Genome Project
(HGP) |
|
|
|
UCSC Genome
Bioinformatics |
|
|
|
Stanford University Genome
Resources |
|
|
Proteomics |
PDB |
Protein
Databank |
|
|
Protein Information Resource
(PIR) |
|
|
Sequence
analysis |
Basic Local Alignment Search Tool
(BLAST) |
Sequence
similarity searching |
|
|
Fasta3
|
FASTA
version 3 at the EBI |
|
|
CLUSTAL
W |
Sequence
alignment |
|
|
WebLogo
|
Alignment
analysis - Sequence logos |
|
|
GenScan |
Gene
prediction and sequence annotation |
|
|
GLIMMER |
Finding
genes in microbial DNA, (bacteria, archaea, and
viruses) |
|
|
CAP EST
Assembler |
Contig
assembling |
|
|
GeneBee |
Predict
RNA secondary structure |
|
|
Translate |
Translates
a nucleotide sequence to a protein |
|
|
Backtranslation |
Translates
a protein sequence back to a nucleotide
|
|
|
TFSEARCH |
Searching
transcription factor binding sites |
|
|
TESS |
Transcription
element search system |
|
|
Tandem Repeats
Finder |
Finds
tandem repeats |
|
|
Eukaryotic Promoter
Database |
|
|
|
WWW Promoter
Scan |
Predicts
promoter regions based on scoring homologies
|
|
|
Promoter |
|
|
|
Primer3 |
Primer
design |
|
|
Web
Primer |
Primer
design |
|
|
OligoArray2 |
Computes
gene specific oligonucleotides for genome-scale
microarray |
|
|
Pira-PCR
|
PCR
Primer design for restriction analysis of
SNP |
|
|
VectorDB |
Vector
database |
|
Pattern
and motif analysis |
PROSITE |
Protein
families and domains |
|
|
Pfam |
Protein
families database of hidden Markov models (HMMs) |
|
|
MotifScan |
Find
motifs in a sequence |
|
|
ChloroP |
Prediction
of chloroplast transit peptides |
|
|
MITOPROT |
Prediction
of mitochondrial targeting
sequences |
|
|
SignalP |
Prediction
of signal peptide cleavage sites |
|
|
NetOGlyc
|
Prediction
of O-GalNAc (mucin
type) glycosylation sites in mammalian
proteins |
|
|
NetNGlyc
|
Prediction
of N-glycosylation sites in human
proteins |
|
|
Myristoylator |
Prediction
of N-terminal myristoylation
|
|
|
NetPhos
|
Prediction
of Ser, Thr and Tyr
phosphorylation sites in eukaryotic
proteins |
|
|
Sulfinator |
Prediction
of tyrosine sulfation
sites |
|
|
REP
|
Searches
a protein sequence for repeats |
|
|
Coils
|
Prediction
of coiled coil regions in proteins |
|
|
The Cambridge Structural
Database |
Small
molecule crystal structures |
|
Prediction
of disordered regions |
DisEMBL
|
Protein
disorder prediction |
|
|
GlobPlot
|
Protein
disorder/order/globularity/domain
predictor |
|
2D
- Protein |
PredictProtein |
|
|
|
nnPredict |
|
|
|
TMHMM |
Prediction
of transmembrane helices
|
|
|
TMpred |
Prediction
of transmembrane regions and protein
orientation |
|
Tertiary
structure (3D) - Protein |
CPHmodels |
Comparative
modeling |
|
|
SWISS-MODEL |
Comparative
modeling |
|
|
Geno3d
|
Comparative
modeling |
|
|
Threader
|
Threading-protein
fold recognition |
|
|
HMMSTR/Rosetta
|
Ab
initio
--prediction
of protein structure from sequence |
|
|
What If
|
For
mutant prediction, structure verification, molecular
graphics |
|
Modeling and visualization
tools |
Swiss-PdbViewer |
|
|
|
Rasmol |
|
|
Systems biology
-Pathways |
KEGG
|
Pathway
maps, ortholog group tables,
etc. |
|
|
Cell Signaling Networks Database
(CSNDB) |
Signaling
pathways of human cells |
|
Systems biology-
Interactions |
Database of Interacting Proteins
(DIP) |
Interactions
between proteins |
|
|
Biomolecular Interaction Network Database
(BIND) |
Interactions
and pathways |
|
|
Protein-Protein Interaction Server
|
The
protein-protein interface
|
|
Systems biology- Protein
localization in cells |
PSORT |
Prediction
of protein localization sites in
cells |
|
|
Protein annotation diagram oriented analysis
(PANDORA) |
Analysis
of protein sets by integration of annotation
sources |
