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The Bioinformatics Portal - Relevant Databases and Web Sources




Bioinformatics Databases and Web Sources

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



 



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