Useful Links for Bioinformatics and Plasmodium Research


Malaria (Forsdyke)
Plasmodium vivax Genome Project
Plasmodium vivax Malaria Index
Plasmodium vivax malaria Index
Cell Biology of Plasmodium
PlasmoDB : Data Sources
PlasmoDB : The Plasmodium genome resource
Apicomplexan Database Resources

My favourite P. vivax-P.falciparum homologous regions, images from PlasmoDB


Bioinformatics links directory

Societies and user groups

International Society for Computational Biology
Australian Bioinformatics Network

Hidden Markov Models

Hidden Markov Model (HMM) Toolbox for Matlab
HTK Speech Recognition Toolkit
HTK - Hidden Markov Model Toolkit - Speech Recognition toolkit


GeneMapper: Reference Based Annotation
The GlimmerM Home Page
The GlimmerHMM Home Page
Sybil: Web-based software for comparative genomics
GeneMark℁ - Gene prediction software programs
GenomeScan Home Page
GENSCAN web server
Twinscan Web Site
The European Bioinformatics Institute
SLAM webserver

ISCB (International Society for Computational Biology)
WEHI Bioinformatics Home Page
Genetic Information Research Institute
Bioinformatics Research Center (BiRC) - BiRC
The Institute for Genomic Research
The Institute for Genomic Research (TIGR) is a not-for-profit center dedicated to deciphering and analyzing genomes-the complex molecular chains that constitute each organism's unique genetic heritage.
NCBI HomePage
The National Center for Biotechnology Information (NCBI) provides an integrated approach to the use of gene and protein sequence information, the scientific literature (MEDLINE), molecular structures, and related resources, in biomedicine.
The Wellcome Trust Sanger Institute
Center for Bioinformatics and Computational Biology
UCSC Bioinformatics Research Projects
bioinformatics computational biology, gene finding RNA DNA, hidden Markov model
CCGB: Miller Lab
Burge Lab, MIT Department of Biology
Forsdyke lab, Queen's University (Canada)
International Max Planck Research School for Computational Biology and Scientific Computing
The R Project for Statistical Computing
R Tutorial (Prof. Norman Matloff, UC Davis)
CRAN (R packages) mirror at University of Melbourne
Fitting Distributions with R
StAR - Statistical analysis of ROC curves
pROC: display and analyze ROC curves in R and S+
Arun Konagurthu's links page
OrthoMCL Database Home
MCL - an algorithm for clustering graphs
FastCommunity (network community with modularity) Aaron Clauset
GraphCrunch - A Tool for Large Network Analyses
ClustRNet: Exploring Biological Network Structure with Clustered Random Graphs
SVINET - identify overlapping communities in large undirected networks by stochastic variational inference
GPU-FAN Gpu-based Fast Analysis of Networks
UC Irvine machine learning repository
Parallel K-Means Data Clustering
Fionn Murtagh's Multivariate Data Analysis Software and Resources
A Little Book of R for Multivariate Analysis
Serafim Batzoglou's Website
Ian Holmes
Ian Korf
Sanger Institute Software
The Artemis Manual
The MUMmer Home Page
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
The Statistics of Sequence Similarity Scores
FASTA at U. of Virginia
The JIGSAW Home Page
Eval Home Page
GBrowse: The Generic Genome Browser | GMOD
PHYLIP Home Page
PHYLIP Phylogeny Inference Package computer programs for inferring phylogenies
ANU Centre for Bioinformation Science (software including PyEvolve and COGENT
RepeatMasker Home Page
Biopython - BioPython
CSB Toolbox - Python structural biology tools
ProDy - Protein Dynamic Analysis in Python
CoreBio - another python toolkit for computational biology (includes STRIDE parser)
Peter's Python Programming Pages
Excellent examples of using BioPython for protein superposition, etc.
Trapped in the USA- Bosco K. Ho (postdoc in protein science, UC San Francisco)
Main Page - BioPerl
UCSC Genome Browser Home
UCSC Genome Browser
Mercator: Multiple Whole-Genome Orthology Map Construction
ROSE: Region-of-Synteny Extractor
Sigma: alignment of non-coding DNA
The GeneSplicer Home Page
SplitsTree 4 - compute evolutionary networks from sequence data (includes NeighborNet)
CD-HIT: cluster large protein db at high sequence identity threshold
Bookshelf - Online books
The NCBI Bookshelf is a collection of biomedical books adapted for the Web with links to Entrez databases.
Molecular Biology of the Cell. Table of Contents
One cannot watch cells crawling, dividing, segregating their chromosomes, or rearranging their surface without feeling curious about the molecular mechanisms that underlie these processes. Alberts, Johnson, Lewis, Raff, Roberts, Walter; Garland Publishing.
Structure-Function Relationships
Graduate Class < Main < Biowiki
Google Scholar via UniMelb proxy
Bioinformatics Journals links
ISI Journal impact factors via UniMelb proxy
GTF2: Mouse/Human Annotation Collaboration: Submission Format
GTF2.2: A Gene Annotation Format
UCSC Genome Bioinformatics: FAQ
UCSC Genome Browser FAQ
Drosophila Annotation Collaboration: Submission Format
IUBMB Nomenclature Home Page
The full text of IUBMB and IUPAC biochemical and organic nomenclature recommendations
Incomplete nucleic acid sequences
The full text of the IUBMB recommendations on nomenclature for incompletely specified bases in nucleic acid sequences
Amino Acid Properties
FASTA format description
Table of Standard Genetic Code
multi-FASTA format description
UCSC Genome Browser: axt Alignment Format

GFF2PS MAIN PAGE: Converting GFF to PostScript.
GFF2PS MAIN PAGE: Converting GFF to PostScript.
Sequence Ontology Python GFF library
The world's largest development and download repository of Open Source code and applications

RNA Topology Database: Program
MAVID multiple alignment server
MAVID multiple alignment server
Pecan: consistency based multiple alignment
Repbase - GIRI
RCPdb: evolutionary classification and codon usage or Repeat Containing Proteins

Network Alignment

MNAligner: Alignment of molecular interaction networks by quadratic programming
Graemlin: General and robust alignment of multiple large interaction networks
netcoffee - a global alignment tool for multiple networks
IsoRank and IsoRankN - global alignment of multiple protein-protein interaction networks

SVG and JavaScript

SVG specification
carto:net - SVG tutorial and example site
JavaScript - MDC
JavaScript & DHTML Cookbook (via UniMelb library online books)

Graphics hardware programming

CAMPAIGN - GPU clustering algorithms
PRNG Random Numbers on GPU (Langdon, UCL)
Harvesting graphics power for MD simulations
Sh - embedded metaprogramming language
GPGPU: general-purpose programming using graphics hardware
NVIDIA CUDA developer home
Write Less Code: Stochastic Simulation Algorithm on CUDA
GPULib - access to GPU from Python, MATLAB, IDL
Mars: a MapReduce framework on graphics processors
cuSVM - CUDA implementation of Support Vector Classification and Regression
MAGMA - GPU and multicore implementation of LAPACK functionality
CULA Tools - GPU accelerated LAPACK functions
Dynamic Creator for Mersenne Twister RNG (used by CUDA SDK Mersenne Twister)
CUSP library for sparse linear algebra and graph computations on CUDA
CUDPP CUDA Data Parallel Primities (includes hash table)
Medusa: Building GPU-based Parallel Sparse Graph Applications with Sequential C/C++ Code

Lock-free algorithms for multicore

lock-free hashtable and other data structures
Hopscotch Hashing (Herlihy et al 2008) implementations at google groups
Bit Twiddling Hacks
Streamflow: a scalable memory allocator for multihreaded applications
Practical lock-free data structures (Cambridge Computer Laboratory)
Intel Thread Building Blocks
Intel Threading Building Blocks for Open Source
OpenMP parallel programming
SDN: Calculating Processor Utilisation From the UltraSPARC T1 and UltraSPARC T2 Performance Counters
Source code for lock-free data structure implementation (POSIX threads and CUDA) ICPDS 2012


Python Programming Language
Home page for Python, an interpreted, interactive, object-oriented, extensible programming language. It provides an extraordinary combination of clarity and versatility, and is free and comprehensively ported.
Python Tutorial
Docutils Project Documentation Overview
Quick reStructuredText
Python Library Reference
Python Infrequently Answered Questions
Numpy Home Page
Numpy example list
numarray home page
SciPy: Scientific Tools for Python
ScientificPython (not to be confused with SciPy)
unPython - Converting Python numerical programs into C
LAPACK: Linear Algebra PACKage
BLAS: Basic Linear Algebra Subprograms
Jack Dongarra's list of freely available linear algebra software
HSL Archive (Harwell Subroutine Library)
ATLAS: Automatically Tuned Linear Algebra System
BeBOP: Berkeley Benchmarking and Optimization Group - inc. OSKI (Optimized Sparse Kernel interface)
Research and software development in sparse matrix algorithms (CHOLMOD etc.)
Stanford Systems Optimization Laboratory free software (MINRES, SYMMLQ, etc.)
PyDot: A Python interface to the GraphViz dot language
NetworkX: Python package for the creation, maninpulation and study of the structure, dynamics and functions of complex networks
RPy: R from Python
PyML: Python Machine Learning package
Matplotlib: a Python 2D plotting library
Sage - open source mathematics software
nlpy - nonlinear programming in python
CVXOPT: A Python Package for Convex Optimization
CVXMOD: Convex optimization software in Python
CVX: Matlab Software for Disciplined Convex Programming
LEMON C++ graph library - part of COIN-OR, inludes Python binding (which seems to be discontinued, doesn't do much anyway?)
MTGL MultiThreaded Graph Library
graph-tool: Python graph library implemented in C++ [however I found Dijkstra here SLOWER than Python implementation, and crashes with stack overflow even on small graphs]
igraph library implemented in C with R and Python interfaces
mlabwrap: a high-level Python to MATLAB bridge
MINQ: General Definite and Bound Constrained Indefinite Quadratic Programming (in MATLAB)
MATLAB Central file exchange: 4 Dimensional visualiation
pycplex: a Python interface to the ILOG CPLEX callable library
Parallel Python
F2PY - FORTRAN to Python interface generator
MPI for Python
MPI Tutorial at LLNL
OpenMP Tutorial at LLNL
Priority Queues (includes link to Fibonacci Heap C source code)
Fibonacci heap code (nonrecursive and efficient)
a module for profiling compiled python extensions
EasyPDP - an efficient parallel runtime system based on DAG data driven model for dynamioc programming
CDE: Automatically create portable Linux applications
SlopPy: An error-tolerant Python interpreter that facilitates sloppy programming
minepy Maximal Information-based Nonparametric Exploration in C, C++, Python and MATLAB/Octave

RNA Structural Alignment

A portal site for functional RNAs and non-coding RNAs — Main Page
miRBase::Sequences (Sanger Institute microRNA data)
Rfam (JFRC)
BRAliBase: Benchmark RNA Alignments
BRAliBase 2.1 (An enhanced RNA alignment benchmark for sequence alignment programs)
Mathias Sprinzl's compilation of tRNA sequences and tRNA gene sequences
5S Ribosomal RNA Database The RNA Structure Database
SCOR: Structural Classification of RNA
NDB: The Nucleic Acid Database
NCIR: a database of non-canonical interactions in known RNA structures
Rfam (Sanger Institute)
S . C . A . R . N . A
BioWiki - Multiple RNA Alignment
DFG Project: Klau and Bauer's research proposal
Structural RNA alignments (FU-Berlin, Bauer)
LiSA Alignment software library
Rimon Mikhaiel research (SPRC)
Naren Ramakrishnan
TCoffee webserver
T-Coffee home page
Vienna RNA Package
NUPACK: Nucleic Acid Package
Zuker Group: Algorithms and thermodynamics of RNA secondary structure
Turner Lab: RNA biophysical chemistry
Eddy Lab: identifying novel structurual and catalytic RNAs
TBI Theoretical Biochemistry Group
The Bioinformatics Center at Rensselear and Wadsworth
Computational Biology/Chemistry/Biomathematics at NYU (Tamar Schlick's group)
Shapiro group at NCI: computational RNA structure group
RNA@IGIB (Institute of Genomics and Integrative Biology (India))
RNA Tools @ LIFL (Laboratoire d'Informatique Fondamentale de Lille), includes Carnac
DART library: Stemloc, XRATE, and more
Consan: pairwise structural RNA alignment
Stockholm format for marking up features in multiple alignments
RSmatch: aligning RNA secondary structures and finding RNA motifs
rna_align (Bin Ma 2000 / Jiang et all 2002 A General Edit Distance Between Two RNA Structures
PMcomp / PMmulti
UNAfold (replaces mfold)>
mfold web server job submission form
Burnet Institute Mfold Server (Melbourne)
KNetFold homepage (Shapiro Group)
RNA As Graphs web resource
The RNA World website
LocARNA (chair for bioinformatics at Freiburg)
ERA - efficient alignment of RNA secondary structures using sparse dynamic programming
ExpaRNA - Lightweight comparison of RNAs based on exact sequence-structure matches
Freiburg Bioinforamtics, inc. Freiburg RNA Tools (inc. LocARNA, ExpaRNA)
CONTRAfold - Conditional Training for RNA Secondary Structure Prediction (also RAF - RNA Alignment and Folding)
RNA Sampler (Stormo lab, WUSTL)
MASTR (multiple alignment and structure prediction of RNA using simulatd annealing)
Pair Hidden Markov Models on Tree Structures
ARTS: Alignment of RNA Tertiary Structures
DIAL - Dihedral Alignment server (RNA version)
RNA FRABASE - RNA Fragment search engine and database
aln3nn - progressive multiple sequence alignment from triplets
Milinkovitch lab (ProAlign)
RNAz - Predicting structural noncoding RNAs
BlockMSA - Biclustering as a method for RNA local multiple sequence alignment
Pfold RNA folding server
MAFFT multiple alignment for amino acid or nucleotide sequences
RNAforester online (Bielefeld University)
A Gentle Guide to Multiple Alignment (Uni-Bielfeld)
VARNA - Visualization Applet for RNA
CentroidAlign -fast and accurate multiple RNA sequence alignmen by maximizing expected SPS
DAFS - simulataneous aligning and folding of RNA sequences by dual decomposition
WAR - webserver for Aligning structural RNAs
PMFastR: A New Approach to Multiple RNA Sturctural Alignment
RNASAlign: RNA Structural Alignment System
RNA-Pareto: Structural RNA Alignment by Multi-objective Optimization

Protein structure

RCSB PDB (Protein Data Bank)
UniProt (Protein sequence and function)
SCOP: structural classification of proteins
SISYPHUS: Structural alignments for proteins with non-trivial relationships
CATH Protein Structure Classifcation Database (UCL)
SCOPCath: Systematic comparison of SCOP and CATH
The DomPred protein domain classification server
SSM Secondary Structure Matching (replaces Dali service 26Jan2008)
VAST Vector Alignment Search Tool
SHEBA (Structural Homology by Environment-Based Alignment
MOMA: Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner
PRIDE2 protein fold similarity server
YAKUNET: a web interface to YAKUSA (protein structure database search)
CMOS Online Server for Protein Structure Alignmente via Contact Map Overlap Maximization
Vorometric: Integrated search and alignment of protein structures using Voronoi contacts
Erebus protein substructure search server
PTGL - Protein Topology Graph library
TOPS++FATCAT - fast flexible structural alignment using constraints derived from TOPS+ strings models
TOPS+ - a novel method for comparing topological models of protein structures enhanced with ligand information
ProCKSI - Protein (Structure) Comparison, Knowledge, Similarity and Information
SABERTOOTH structural alignment of protein folds
MAMMOTH protein structural alignment server
ALADYN dynamics-based alignment of proteins
Combinatorial Extension (CE) for protein structure comparison and alignment
Brutlag bioinformatics group at Stanford (LOCK2, etc.)
SARST - Structural similarity search Aided by Ramachandran Sequential Tranformation
3D-BLAST protein structure search
CLePAPS - Fast Pair Alignment of Protein Structures Based on Conformational Letters
Fr-TM-align download (Skolnick group at CSSB Georgia Tech.
PPM: Protein structure alignment considering phenotypic plasticity
The ASTRAL compendium for sequence and structure analysis
PDBsum: overview of structures depositied in the PDB
PDB Lite
Nh3D: a reference data set of non-homologous protein structures
PROTEUS, including Proteus_300 MAX-CMO test data set
DSSP protein secondary structure
STRIDE homepage
PALSSE: Predictive Assignment of Linear Secondary Structure Elements
TOPS source code
Glasgow TOPS server
Pro-origami: Protein structure cartoons
TopDraw (Charles S. Bond)
mmLIB: Python Macromolecular Library
RCSB PDB software tools
PDBCharmer (another Python PDB parsing module)
pdb-tools: command-line python scripts for manipulating PDB files
PyMOL wiki
Creating publication quality images with PyMOL
PyMOL Ray tracing
VMD: Visual Molecular Dynamics
VMD atom selection language
Jmol: an open-source Java viewer for chemical structures in 3D
MGLTools: Python Molecular Viewer (PMV), AutoDock, MolKit, etc.
World Index of BioMolecular Visualization Resources
MolKit - (includes yet another PDB parser etc., but can build secondary structure from HELIX and SHEET cards and from STRIDE
Another python parser for PDB files
Thomas Hamelryck (University of Copenhagen Bioinformatics Centre)
University of Leeds Bioinformatics group (includes Westhead group; TOPS, Helix Packing Pair, etc.)
HB plot
Protein structure bioinformatics group at Reading (Dr Gail Hutchinson)
Dr Gail Hutchinson (University of Reading)
HELANAL, characterize alpha helix geometry
QHELIX: a computational tool for the improved measurement of inter-helical angles in proteins
Kinemage (Richardson Lab at Duke)
Richardson 1981 The Anatomy and Taxonomy of Protein Structure
DDOMAIN server
Protein Domain Parser (PDP) (Alexandrov and Shindyalov)
pDomains: Benchmarking and analysis of structural domains in proteins
Protein domain server ('AUTHORS') (Islam et al)
Vienna University Biomolecular Structural Chemistry (Carugo 2007 domain decomposition software)
Zhou lab (computational biology at Indiana University School of Medicine
(Origami) Folding and Unfolding (Erik Demaine)
Origami Mathematics
Robert J. Lang origami
Paul W. K. Rothemund - DNA origami
SSS Super-Secondary Structure database
UNSW Quantitative and Computational Biology (Prof. Marc Wilkins)
BioMolecular Modelling Laboratory (Cancer Research UK London Research Institute)
Geometry (Paul Bourke, UWA)
PAST - Polypeptide Angles Suffix Tree
MALISAM: Manual ALIgnment of Structurally Analogous Motifs
TableauSearch supplementary material for paper
GANGSTA: Genetic Algorithm for Nonsequential and Gapped Structure Alignment
deconSTRUCT server
CLICK Topology Independent Comparison of Biomolecular 3D Structures
TOPOFIT db: a database of protein structural alignments based on the TOPOFIT method
SCALI: Structural Core ALIgnment of proteins
FelxSnap download
SALAMI: structure alignment and match inquiry
TopMatch webserver
ProSMoS server
OPAAS server
IPSA: index-based protein substructure alignment
MISTRAL - energy based protein multiple structural alignment
ProtMot - PROTeins MOTif analysis tool
DEDAL protein structure alignment
COPS - Classification of Protein Structures
COPS Benchmarks for protein database search
HOMSTRAD Homologous Structure Alignment Database
SABmark - Sequence and structure Alignment Benchmark
Theseus - An application for maximum likelihood superpositioning and analysis of macromolecular structures
EVfold - from evolutionary constraints to 3d structures
ppsAlign - parallel protein structure alignment on GPGPUs (paper)
VPLG - The Visualization of Protein-Ligand Graphs software package
Kpax - Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment assembly
SAS-Pro: Simultatneous Alignment and strugure Superposition of PROteins
MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments
GPU-CASSERT - parallel implementation of protein 3d structure similarity on GPU and CUDA
GrAlign - Aligning Protein Structures with Graphlet-based Aligner
Michael Petitjean: The Mathematical Theory of Chirality

X-ray Crystallography

Randy J. Read's home page
Phaser crystallographic software homepage
Protein Crystallography Course
Kevin Cowtan's Book of Fourier

Quadratic Programming, Mixed Integer Proramming, SAT, etc.

QAPLIB - A Quadratic Assignment Problem Library
Ant Colony Optimization
Prof. Eric Taillard
MiniSat: Open-source SAT solver
SAT solving in Prolog: interface SWI-Prolog to MiniSat
SCIP: Solving Constraint Integer Programs
A Quadratic Programming Page (Gould and Toint)
Galahad - a thread-safe library of Fortran 95 packages for solving nonlinear optimization problems (including QP)
Ipopt - Interior Point Optimizer for large-scale nonlinear optimization
ParamILS - Automatic Algorithm Configuration based on Local Search
FADBAD++ Flexible Automatic differentiation using templates and operator overloading in C++ Community Portal for Automatic Differentiation

Dynamic programming

Bellman's GAP Declarative Dynamic Programming for Bioinformatics

Dynamic programming problem data sets

9th DIMACS Implementation Challenge - Shortest Paths
Pisinger's optimization codes (Knapsack Problems)
Constraint Modelling Challenge 2005 (Open Stacks)

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