Links
Nucleotide Sequence Databases
- NCBI – National Center for Biotechnology Information
- EBI – European Bioinformatics Institute
- DDBJ – DNA Data Bank of Japan
Protein Sequence Databases
- SWISS-PROT & TrEMBL – Protein sequence database and computer annotated supplement
- UniProt – UniProt (Universal Protein Resource)
- HUPO – HUman Proteome Organization
Database Searching by Sequence Similarity
Sequence Alignment
- ClustalW @ EBI – multiple sequence alignment
Genome Databases
- Ensembl – automatically annotated human genome
- TIGR Microbial Database
- The Proteome Databases – yeast, worm, & human, good annotation
- Saccharomyces Genome Database
- WormBase – C. elegans
- FlyBase
- Berkeley Drosophila Genome Project
- Mouse Genome Informatics
Protein Domains: Databases and Search Tools
- InterPro – integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL
- PROSITE – database of protein families and domains
- Pfam – alignments and hidden Markov models covering many common protein domains
- SMART – analysis of domains in proteins
Protein 3D Structure
- PDB – protein 3D structure database
- RasMol / Protein Explorer – molecule 3D structure viewers
- SWISS-MODEL – homology modeling server
- DALI – 3D structure alignment server
- Jpred2 – protein secondary structure prediction
Phylogeny & Taxonomy
- The Tree of Life
- TreeView – user friendly tree displaying for Macs & Windows
Gene Expression Databases
- HuGE – database of human gene expression using arrays
- Stanford Microarray Database
- Gene Expression Omnibus (GEO)
Metabolic, Gene Regulatory & Signal Transduction Network Databases
- KEGG – Kyoto Encyclopedia of Genes and Genomes
- DAVID – Database for Annotation, Visualization and Integrated Discovery
Systems Biology
Systems biology-funded centers
Computational Resources
- CPAN – PERL modules
- bioperl – bioinformatics related PERL modules
- C++ Standard Template Library Programmer’s Guide
- C++ Annotations
- GNU C Library Reference
- C Tutorial
- Java Tutorial
- Numerical Recipes in C and Fortran
- Dictionary of Algorithms, Data Structures, and Problems
- The Linux Cookbook
Bioinformatics on-line course materials and tutorials
Intro to bioinformatics and computational biology:
- Introduction to Bioinformatics (Technion – Israel Institute of Technology)
- Introduction to Bioinformatics (UCSD)
- A taste of bioinformatics (University College London)
- Introduction to Computational Molecular Biology (Washington University in St. Louis)
- Introduction to Bioinformatics (UCSD Extension)
- Computational Biology (University of Washington)
- Introduction to Computational Biology (Carnegie Mellon University)
- Introduction to Computational Molecular Biology (MIT)
- Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis (University of Washington)
Algorithms:
- Algorithms in Computational Biology (Technion -Israel Institute of Technology)
- Algorithms for Molecular Biology (School of Mathematical Sciences at Tel Aviv University)
Miscellaneous:
- Elementary Sequence Analysis (McMaster University)
- Dynamic Programming Tutorial (By Eric C. Rouchka)
- Beginner’s Guide to Molecular Biology (Rothamsted Research)
- A Primer on Molecular Genetics (Iowa State University)
- Online Lectures on Bioinformatics (Max Planck Institute for Molecular Genetics)
- EMBnet.org Courses (EMBnet.org)
- DNA and Protein Sequence Analysis (Boston University)
- Computational Molecular Biology (Stanford University)
- Current Topics in Genome Analysis (handouts) (NIH)
- Current Topics in Genomic Analysis (on-line video) (NIH)
- Bioinformatics and Genomic Analysis (University of Arizona)
- Biological Data and Analysis Tools (UCSD)
- Introduction to Structural Bioinformatics (UCSD Extension)
- Object-Oriented and Database Programming for Bioinformatics and Internet ( Feinberg Graduate School of the Weizmann Institute of Science, Rehovot, Israel)
- Computer Skills For Biologists (UCSD Extension)
- An Intro to R (UMN)
- Statistical Computing with R: A tutorial
- Matlab Tutorial
- Matlab Tutorial (Elementary)
- Microarray Data Analysis