Ten important bioinformatics databases
Twelve important software programs in bioinformatics
Ten bioinformatics resource locators
Essential Websites
DNA chips and micro-arrays
Genomic information
Protein sequences
Biochemistry
Biochemical pathways and enzymes
3-D structure information resources
Specialized protein databases
| Address | Description |
| imgt.cines.fr | IMGT, the International Immunogenetics database, specializes in proteins involved in the immune response. |
| rebase.neb.com | Rebase, the reference restriction-modification enzyme database. |
| afmb.cnrs-mrs.fr/CAZY | CAZy, an information resource on enzymes that degrade, modify, or create glycosidic bonds. |
| www.merops.co.uk | MEROPS, a database specializing on proteases. |
| pkr.sdsc.edu/html/index.shtml | PKR, the Protein Kinase Resource, focuses on the protein kinase family of enzymes. |
| nrr.georgetown.edu | NRR, the Nuclear Receptor Resource, is a collection of individual databases on the steroid and thyroid hormone receptors. |
| senselab.med.yale.edu/senselab | The Human Brain Database provides information on the proteins involved in neural processes, such as ion channels, membrane receptors of neurotransmitters and neuromodulators, as well as olfactory receptors (ORDB). |
| www.ncbi.nlm.nih.gov/COG | The COG (Cluster of Orthologous Groups) database regroups proteins shared by at least three major phylogenetic lineages (ancient conserved domains). |
DNA analysis
Searching motifs in DNA sequences
Main protein motif and domain collections sites
Protein sequence analysis over the Internet
ExPASy servers around the world
BLAST and PSI-BLAST servers around the world
Alternative methods for homology searches
Various flavors of dot-plot programs
| Name | Used For | Range | Platforms |
| Dotlet | Proteins, DNA | 10,000 | All |
| Dnadot | Proteins, DNA | 100,000 | All |
| Dotter | Proteins, DNA | 100,000 | Unix, Linux, Windows |
| Dottup | Complete genomes, DNA | >100,000 | Unix, Linux |
Online pairwise alignment programs
Online pairwise alignment analyses
BLAST servers integrating multiple alignment methods
ClustalW servers
Other multiple sequence alignment resources over the Internet
Motif-finding methods available online
Sequence text conversion on the Web
Multiple sequence alignment editing packages
Extracting information from a multiple sequence alignment
Multiple alignment beautifying tools
Predicting secondary structures
Some RNA analysis resources
Ribosomal RNA resources on the Internet
| URL | Description |
| rdp.cme.msu.edu | Provides data and services, including online phylogenetic analysis. |
| rrna.uia.ac.be/lsu | A European database on the larger of the two ribosomal subunits. It contains predicted structures. You can query the database online. This site features lots of online software. |
| rrna.uia.ac.be/ssu | Dedicated to the small ribosomal subunit. |
Some non-coding RNA resources
Generic RNA resources
Phylogenetic trees
Generic phylogenetic resources on the Internet
Collections of orthologous sequences
Ref: Bioinformatics For Dummies