Databases and Web Resources
for Sequence Analysis

Wei-Jen Lin
Cal Poly Pomona

 

Tools for Sequence Analysis
Web Databases
Web Resources and Tools

 

Sequence Analysis Tools

Comprehensive Tools
DNA Sequence Analysis

Biology WorkBench
A web server supported by UCSD Supercomputer Center

pDRAW
Free softwares for DNA sequence analysis and graphics

BCM Search Launcher
A web server supported by Baylor College of Medicine

Institute Pasteur Biological Softwares
A web server for a variety of sequence analysis tools

Biological Information Resource (BIR)
A web server supported by U. Washington

EMBOSS
The European Molecular Biology Open Software Suite which provides free analysis programs in the Unix platform; some programs can be accessed through web servers listed above

IUBio Archive
An archive of Biology Data and Software
organized by the Indiana University

EMBL Archive
FTP files of free softwares

Sequence Retrieving
Entrez - NCBI
Access database - EMBL
SRS - DDBJ
Format Converison
Reverse and Complement
REVSEQ
Mw, Tm Determination

Tm determination
DAN
Genset Oligos calculation
Conversions for Molecular Biology
BioPolymer Calculator

Restriction Enzyme Analysis

SeqCUTTER
Webcutter

NEBcutter
REbase - a restriction enzyme database

Translation and Codon Usage
DNA Translation
Protein Engine
Codon Usage Database
Genetic code Table
PCR Primer Selection
Prime3
DoPrimer
RNA/DNA Secondary Structure
mfold
Merge Two Sequence
Merger - EMBOSS
Sequence Alignment
BLAST/NCBI
Dot Plot
Clustal W (1.60) 
Phylogenetic Analysis
PHYLIP
Clustal W (1.60)
Pattern Search
CpGreport - CpG rich regions
Prosite/EMBL - pattern search
PatScan - pattern search
Genome Analysis

ORF Finder /NCBI
Gene mark

Grail
GENSCAN -MIT
MZEF - Cold Spring Harbor
Banbury Cross - A list of links to gene identification softwares
GeneMachine
- An integrated tool intended to perform both comparative and predictive gene identification techniques
Signal Scan - transcriptional elements
Promoter Scan 

Protein Sequence Analysis
Basic Analysis
Pattern Search
Structure and Function

SAPS 
pI/Mw
ProteinProspector
Reverse Translator
PHYLIP - phylogenetic analysis
PSORT - Predict protein localizations in cells
Multiple Sequence Alignment - crtree, clustalw, MSA
Blast/NCBI - sequence alignment

Blocks - conserved homologs
Prosite/EMBL - pattern search
PatScan - pattern search
SignalP - signal peptide
Pratt - protein motif
PEST - P.E.S.T. degradation sites
DIGEST - protease cleavage sites
NetOGlyc - glycosylation

Structure/NCBI
ExPASY -proteomic tools
BioCoRE - Univ. of IL-UC
Links to 3-D Structure Viewers
Dali - structure alignment
nnPredict -secondary structure
PHD -secondary structure
ProDom - domain database
Pfam - protein family alignment database
BCM Protein Secondary Structure Prediction
TOPS - topology 

Web Databases

Major Sequence Repositories
Genomic Databases
Protein Databases

Genbank
DNA and protein sequence database maintained by National Center for Biotechnology Information (NCBI)

EMBL-EBI (European Molecular Biology Laboratory)
DNA and protein sequence database maintained by European Bioinformatics Institute (EBI)

DDBJ (DNA Data Bank of Japan)
DNA and protein sequence database maintained by DNA data Bank of Japan

NCBI
Views of chromosomes and maps and loci with links to other NCBI resources

Ensembl
Allows access to genome databases with automatic analysis and software. A joined project by EMBL and Sanger.

Sanger Institute
Allows access to the updated genome sequences done at the institute

TIGR (Institute for Genomic Research)
Gene Indices of a variety of species including human, animals, plant and microorganisms

University of California at Santa Cruz
Contains the assembly of the draft human genome sequences

Washington University
Contains links to clone and accession maps of the human genome

RIKEN/University of Tokyo
Gives an overviews of the entire human genome structure

Celera
Access to sequence and tools for human genomics

Molecular Biology Database Collections Table
Nucleic Acids Research, 2001, Vol. 29, No. 1, p1-10
Updated in every January issue

 

 

ExPASy Life Science Directory
List of a variety of databases

SWISS-PROT
Curated protein sequences; motif search including sites for protease, glycolysis and Zinc fingers

PIR (Protein Information Resource) - protein sequence database

PDB (Protein Data Bank)
Structure data determined by X-ray crystallography and NMR

MMDB (Molecular Modeling DataBase)
Protein structures linked to NCBI Entrez

Web Resources and Links

NHGRI Talking Glossary

Virture Library of Genetics/ORNL
includes information and links on bioinformatics, databases, and related topics

The Bio-Web
A web resource for molecular and cell biologists

Harvard BioLinks

Cold Spring Harbor Laboratory Sequence Analysis on the Web

Healthlinks - Molecular biology toolkit, U. Washinton

ExPASy Life Science Directory
Extensive lists of links to protein and DNA databases and resources

Oak Ridge National Laboratory (ORNL)
Java viewer of human genome sequence; tools for analysis and annotation

Science Functional Genomics
including links to web resources, online glossaries and articles; Timeline of Genomic History

NHGRI
Contains information, links and articles on a wide range of social, ethical and legal issues