Bioinformatics Resource

Tutorials on the Web

On-line tutorials for BLAST, Entrez, PubMed, Map Viewer, and Structure at NCBI
BLAST Search Tutorial
PSI-BLAST Search Tutorial
Online Inheritence In Man (OMIM) Tutorial
Principles of DNA Arrays (animated)
EST (Expressed Sequence Tag) Primer
SNP (Single Nucleotide Polymorphism) Primer
MALD/TOF: Introduction to Methods and Principles

Major Bioinformatics Sites

NCBI Biocomputing Resources (my favored site)
Extensive selection of databases and search tools. Easy maneuvering and download of interesting data. Best BLAST tool.

European Bioinformatics Institute (EBI)
Offers a full line of services: EMBL Nucleotide Sequence Database. SWISS-PROT and PIR Protein Sequence Database. Data Submission. Database query/retrieval. Sequence Similarity Searches. Documentation and Software.

Computational Molecular Biology at the NIH
WWW-based Sequence Analysis Services. Databases for Molecular Biology. DocumentationRelating to Sequence Analysis. Molecular BiologyDesk Reference. Repositories of Molecular Biology Software. Other Molecular Biology Resources.

ExPASy
Molecular Biology Server of the Geneva University Hospital and the University of Geneva. For use of the follwing databases: SWISS-PROT. PROSITE Dictionary of protein sites and patterns. SWISS-2DPAGE Two-dimensional polyacrylamide gel electrophoresis database. SWISS-3DIMAGE 3D images of proteins and other biological macromolecules. ENZYME Enzyme nomenclature database. SeqAnalRef Sequence analysis bibliographic reference database.

PubMed
Free access to and retrieval from Medline database.

Bioinformatics Tools

EMBOSS
A large program suit which essentially replaces the discontinued GCG software package of the University of Wisconsin. Easy-to-operate graphical interface.

ORF Finder
A simple tool with a graphic display to find open reading frames in a DNA sequence.

Translation Tool
A nice Java-based translation tool to translate DNA into protein, with graphical overviews.

Codon Usage
Build a codon usage table for every organism that is represented in the genomic database. A good Japanese site.

JAligner
A good Java-based tool for pairwise alignments by the Smith-Waterman algorith.

Dotlet
A Java-based tool for dot plots, excellently made. Explore this tool.

SOSUI Membrane Helix Prediction
Nice tool to predict transmembranous helices in proteins. Also shows helical wheels of membrane helices.

Motif
A good Japanese site to search for motifs in protein and DNA sequences with Prosite, BLOCKS, ProDom, and Pfam, also in Hmmer format.

Swiss-Quiz
Win a Swiss chocolate.

PSort Prediction
Predicts the intracellular localization of bacterial and eukaryotic proteins.

Helic-Turn-Helix Motif Prediction
Predicts helix-turn-helix motifs typical of repressor proteins.

ProtParam
This tool predicts molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of
hydropathicit for a protein.

ClustalW/Jailview Alignment
A site which combines ClustalW multiple alignments with the Jailview display tool. Limitless possibilities to display and color your sequences!

Aldente and Mascot
Programs to identify proteins based on mass spectroscopy data.

Specialty Databases

Genetic Codes
Organism specific use of the genetic code with comments on key features.

SAGE
A database of gene expression data derived by serial analysis of gene expression (SAGE).

Molecular Portraits of Human Breast Tumors
A database of human breast cancer DNA arraying data.

SGD
The yest resource of gene expression/DNA array data.

HapMap Project
A database on SNPs by an international consortium.

SNP Database at NCBI

TIGR: Genome projects, completed and in progress
Listing and/or links to all genome sequencing projects, completed or in progress (TIGR Database)

PDB Browser
Search structural database and download structure files for a 3D viewer, such as RasMol.Or configure your browser to view 3D files directly with Chime!

GenomeNet Japan
Specialty databases for Bacillus subtilis. CyanoBase for Synechocystis. Abberant splicing database. KEGG Encyclopedia of genes and genomes.

WFCC World Federation for Culture Collections
The "Yellow Pages" for Microbiologists.

Glossary at the Human Genome Project Information site.

Tool and Database Collections

Bioinformatics resources, University of Birmingham
A nice collection of specialty bioinformatics tools.

SRS Database Browser
Find tools and databases for anything and everything.

Google
This universal search engine is always a good option to find something.

 Software Tools to Download

Gene-Doc
This program makes nice, publication ready sequence alignments from a GCG sequence alignment (msf file).

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Last updated: November 6, 2009