Bioinformatics links

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Source material

Bioinformatics related blogs

Databases

General

Genomes

Lists of genomes in progress

Genes / Proteins

Web servers

Catalytic Site Atlas (CSA) 
a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
SiteEngine 
Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
ASTRAL 
The ASTRAL Compendium for Sequence and Structure Analysis.
MolMovDB 
Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
Dali Fold Classification 
based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
PDBsum 
provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank
BLOCKS 
a service for biological sequence analysis
Animators 
Visualization tools for the Wright-Fisher model and continous time coalescent.
CombAt 
Comparison of coding DNA that takes the encoded proteins into account.
distanceP 
Predict distance constraints between amino acids in proteins from the amino acid sequence.
FaBox 
FASTA online toolbox
FOLDALIGN 
Find the most significant common sequence and structure motifs in a set of RNA sequences.
GeMprospector 
Find cross-species genetic marker candidates online from a collection of plant ESTs.
Hudson 
Simulation of sequence evolution using the Hudson coalescent process to make a phylogony and the Jukes-Cantor substitution process.
MatrixPlot 
Generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates, and plots of user provided matrix files.
Phy·fi 
Online tool for drawing Newick trees in color. Supports the JPG, GIF, PNG, TIF, PDF, and EPS formats.
PriFi 
Suggest primer pairs based on a DNA sequence alignment and give an account of the quality of the suggested primers.
RecPars 
Phylogenetic analysis using a parsimony analysis that takes recombination events into account.
Rateshift analysis 
Find signs of functional divergence as evidenced by shifts in evolutionary rates between two DNA, RNA or protein sub-families.
RetroSearch 
Database of ORF annotated human endogenous retroviruses.
RNA DB Tools 
Collection of tools which can be used to perform semi-automated update of RNA structural databases.
RNA Folding 
Find common secondary structures for multiple RNA sequences.
SLASH 
Stem-Loop Align SearcH. Search for a common stemloop motif in a relatively large data set.
StatAl 
Statistical alignment of DNA/protein sequences.
SRPDB 
Signal recognition particle database.
tmRDB 
tmRNA database ([1])

Downloadable Software

Blossoc 
Block-Association Mapping.
ClustalW Wrapper 
The clustalw python module contains code for wrapping the ClustalW multiple sequence alignment tool. Bundled with the ClustalW wrapper is also modules for reading FASTA and GDE files.
CoAnnealing 
Simulated Annealing Search for Coalescent Trees.
CoaSim 
Simulating the coalescent process.
ComAlign 
Multiple alignment method that combine alignments toconstruct a good multiple alignment.
CombiBlock 
CombiBlock computes various versions of Hudson and Kaplans(1985) "minimum number of recombination event" statistics, RM, based on the Four-Gamete-Test. Further the programreturns a division of the data into blocks.
Detector 
Codon-based method for detecting changes in environmentspecific selection regimes.
DPROG 
A domain specific language for specifying dynamicprogramming algorithms; given a recursive definition of the problem,the compiler generates code for solving the problem using dynamicprogramming.
Drawtree 
Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.
EvoGene 
Gene finding with a Hidden Markov Model of genomestructure and evolution.
GenePair 
The GenePair package implements a range of comparitive methodsfor gene structure prediction in homologous sequences.
GeneRecon 
A coalescent based tool for fine-scale association mapping.
HapCluster++ 
HapCluster++ is a software package for association mapping.
HMMcomp 
Comparison of hidden Markov models.
QDist 
Computation of the quartet distance between evolutationary trees.
QuickJoin 
A tool for fast neighbor-joining tree construction.
RBT 
A tool for fast construction of refined Buneman trees,
Split-dist 
Split-Dist calculates the number of splits (edges) that differs for two trees.
SuffixTree 
The SuffixTree python module contains code wrapping a suffix tree implementation by Dotan Tsadoc and Shlomo Yona.

Data acquisition (search engines)

Keyword

Similarity

Multiple sequence alignment

Prediction

Phylogenetic analysis

Taxonomy

Software / Scripts

Other

jaMBW 
JaMBW, the Java based Molecular Biologist's Workbench.
SeWeR 
SeWeR: Sequence Analysis using Web Resources is an integrated portal to commonly used bioinformatics tools on Internet and World Wide Web.
SMS2 
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.

Wikis related to Bioinformatics

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