ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.

A python module for parsing ABI trace file (and hopefully ABI gel file too in the not-so-distant future).

Gene finding accuracy evaluation tool and test datasets. It allows a nearly complete set of evaluation statistics to be easily generated on a customisable set of test sequences. AcE has nothing to do with ACEDB. You can download the program 'ace.pl' an

A C++ library of efficient algorithms for bioinformatics

Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis.

Aminonet tool takes pdb file as input form local machine or from http://www.pdb.org and calculates different parameters of the network. Using AmonoNet one can visualize the network in an interactive way.

This group provides ANEX(_P), a program package to compute probability distributions of alternative MSAs by exploring neighborhoods of an input MSA. The probabilities are computed under genuine sequence evolution models with realistic indels. (FTP only)

AnnHyb is a free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers, etc.

AnovArray is a set of SAS macros for the Analysis of Variance of Gene expression. It can be applied to the quantification of biological and technological variation and to the identification of differentially expressed genes in two or more conditions.

ANTHEDNA is a package of integrated UNIX freeware tools for retrieving and analyzing sequence data. It is called ANTHEDNA because it was developed for analyzing the DNA sequence data obtained from the ribosomal database project.

AntisenseML integrate sufficient information to provide fast, flexible access to the data. Moreover,XSLT transformation was made to render the antisenseML file into HTML view.Some useful tools to create update antisenseML will be released soon

Please visit http://bioinformatics.org/arrayalizer/ to see our website and for a detailed description of Array-A-Lizer - A serial DNA microarray quality analyzer. Executables and sourcecode of the project are also available at the website.

A group dedicated to facilitating co-evolution analysis of proteins and/or nucleic acids. Provides open-source, user friendly software to allow researchers with little bioinformatic or programming experience to determine co-evolution in molecules of inter

Asterias is a set of web applications for the analysis of genomic (and, to a lesser extent, proteomic) data that cover from data normalization to development of prediction models for survival data.

This is a windows based base sequence editor. Search, complement, XNA to amino acid,amino acid to XNA,3 to1 & 1to 3 letter code, invert, find ORF,statistics of bps,2bp palindromes

The BatCave will be an integrated database that allows end users to navigate and visualise their methylation data with ease, specifically data generated by the programme 'Batman' (Bayesian Tool for Methylation Analysis).

Bayallele is a Java-based application that uses bayesian inference and markov chain monte carlo methods to analyse genetic data. The analysis revolves around obtaining separate estimates of population size and migration rate for the sampled populations

Bio-Linux 8 is a powerful, free bioinformatics workstation platform that can be installed on anything from a laptop to a large server, or run as a virtual machine. Bio-Linux 8 adds more than 250 bioinformatics packages to an Ubuntu Linux 14.04 LTS base.

Bio-Wave is a Wavelet based semantic pattern & relation extractor and visualizer. It can be used for sequencing, pattern recognition, curve fitting and other similar processes, especially in gene sequencing and tissue viz. problems.

Project Definition: Development of computational tools such as algorithms, software and databases for the collection, interpretation and dissemination of the vast quantities of complex mapping and sequencing data that are generated by human genome res

BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org.

BIOBROWSER is a portal to the existing bioinformatics universe. It encompasses in itself hyperlinked nodes to all major nucleotide, RNA, Protein sequences along with structural and genomics databases to name a few. Also links major related servers.

The BioC# Project is an open-source project dedicated to providing C# tools for processing biological data. The BioC# library will provide a foundation upon which both free software and commercial packages can be developed.

BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparis

BioCocoa is an open source OpenStep (GNUstep/Cocoa) framework for bioinformatics written in Objective-C. We intend to provide OpenStep programmers with a full suite of tools for handling and manipulating biological sequences.

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.

This is a unique project that tries to make an informatic simulated system from a genetic /physiology well-known system.

bioLegato is a programmable graphic interface capable of handling a wide range of data types. Each bioLegato is an "Object". The canvas area allows the user to view and manipulate the data. The menu area runs external programs, which correspond to the met

Bioinformatics tools for performing wavelet analysis on DNA sequences

In order to avoid re-inventing the wheel, a collection of FORTRAN code that may be useful for your scientific program.

This BioPHP project aims to develop modules and, eventually, sample applications for bioinformatics in PHP both for web AND standalone applications (PHP's utility outside of the web is often overlooked.)

BioQuery provides a single, powerful user interface for building search strategies to multiple biomedical databases, and provides a full update service that sends you new data matching your search criteria when new entries are added to the databases.

BIOSEG is a biological interval type for PostgreSQL. A PostgreSQL GiST index is used to improve the speed of overlap, contains and contained-in queries. Note: This project is now un-mantained as PostgreSQL 9.2 and later include a built in range type.

BIRCH bundles together many of the most commonly-used bioinformatics programs, unified through a graphic interface. BIRCH is designed to simplify the task of managing a bioinformatics core facility, but can also run on a single PC.

An easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.

Fast and easy to use script producing a graphical overview of blast results.

Blogo is intended to be a kind of sequence logo generator that detects and displays biological position-specific sequence bias with reduced background noise.

A perl script that assembles families of orthologous genes by parsing a phylogenetic tree reconstructed from a mixture of orthologs and paralogs for a set of n taxa. Given a tree as input, the script reports families of orthologs, and it lists in- and out

BSQuery 1.0 desktop utility that can be used to instantly retrieve sequence annotations from GenBank and other documents (e.g. AGAVE, etc),regardless of the document?s location (a local computer, LAN-based server, online, etc)

The BTL provides generic mathematical components that allow C++ programmers to more rapidly construct applications that model biological entities.

CalPred is a "tool for EF-hand calcium binding protein prediction and calcium binding region identification" using machine learning techniques. It is a free web based software package and is accessible via world wide web from various platforms.

The project "Cancer genome architecture effects on lineage selection" analyses the constraints of the genome architecture on somatic cancer evolution. It can be considered an analogy to the concept of “evolvability” in Darwinian species evolution.

CATCH is an tool for exploring patterns in ChIP profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The tool has a user-friendly graphical interface.

CD-HI/CD-HIT clusters protein sequence database at high sequence identity threshold. This program can remove the high sequence redundance efficiently. Program written by: Weizhong Li

Celutil is an utilty to read&write, compare, convert, query Affymetrix CEL file in binary & ASCII format, gzipped or not. Celutil is a linux command line written in C++ and should compile and run on windows, MacOsX. Based on Affy File parsers & zlib.

Chromhome (http://www.chromhome.org) is a database of comparative genomics showing maps of chromosome homologies across species.

CMView is a software tool written in Java which provides functionality for viewing, analyzing and modeling protein contact maps.

A web-based program that processes and displays information from the Codon Usage Database in an easy-to-read format. Analyze which codons your organism likes to use.

WE strive to provide simple solutions for everyday life in a molbio lab

A web-based program for comparing sequence conservation patterns to three-dimensional structures.

A program to predict secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequence. This program is based on the critical random networks method.

Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes.

A Linux-based system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices.

DeltaStat performs statistical calculations on data from 2D gel experiments quantified in Delta2D. DeltaStat combines the power of R with the efficiency of a database to handle the large amounts of data generated in proteomics experiments.

This project aims to develop programs to DEtect Negative SElection on Recurrent Mutations. Currently, it provides a package, DENSERM_P (version 0.3), which consists of Perl scripts and modules, aided by several shell scripts. Available at FTP repository.

A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors.

Providing tools for QFISH using free software (macros for NIH image) with examples of processed images; methods to calculate mean TRF length by southern blot with image processing and source code of macro for densitometry; and presentations

Software and data for design of selector assays for targeted resequencing applications. The software is a Java and Perl pipeline that performs the tasks required to design selector probes for the coding regions of a set of target genes.

Program to visualise patterns in DNA and RNA by using Chaos Game Representation

A Xubuntu Linux based virtual machine Bioinformatics environment.

This is portable and stable branch of the E-CELL project. Linux, Solaris, and MS-Windows versions are under developping. You will be able to run ecell2 not only in interactive mode but also in batch mode.

Tools in Measuring, Monitoring and Analysing Bio-Diversity. The project's goal is to study software solutions that will aid and will be used to find, visualize, analyze the information and most importantly, communicate it to other people around the globe

EmblEx is a tool to retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries (ASCII files). Users can define complex keywords (or regular expressions) to be searched for. Many outputs are also possible.

EnzymeLab is a program for the numerical and graphical analyses of enzyme kinetics data: the Micaelis-Menton parameters, inhibitor studies (both linear and non-linear), reaction rate/order and mechanism, and assay development/validation.

Epistatic MAPs(E-MAP) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. This project contains applications for imputing / predicting missing values in E-MAP datasets.

ESPSim is an open source JAVA application designed to compute the similarity of protein electrostatic potential maps.

ESP is a flexible platform to evaluate the discrimination abilities of user-defined expression signatures. Besides, it offers individual prediction information that could be useful for clinically prognosis and clinical management decisions.

FirstGlance in Jmol is a simple, free, browser-based tool for macromolecular visualization. It easily shows you the main features of any published macromolecular model (PDB file). It runs on all common browsers and platforms.

FLIMS is reborn. I will be providing small UI components and code snippts that should add up to an application. The general purpose is to build a framework for bioinformatic programming. Maybe hooks into BioRuby and touching on experimental technologies s

FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.

FragSize is a software tool designed to help molecular biologists in DNA band size determination. It use an graphic user interface, so, use FragSize is very easy. Just load the gel image and make the determinations.

FreeMOL is a compilation of free and open source programs forming a framework for computational chemistry, informatics, structural biology and graphics.

fs_kit is a force spectroscopy toolbox, containing programs to fit, align and analyze spectra. It is currently a work in progress. The current state is best described as beta version.

G-language GAE is a software package aiming to provide a generic development and analysis environment for the analysis of complete genomes. (Development at Bioinformatics.org is discontinued. Please proceed to the home page at http://www.g-language.org/.)

GAUTAM ORF FINDER is a web-based program written in perl script in 2008 to find ORF present in any DNA sequence. User has to just input any DNA sequence i.e. ATGC... and within fraction of seconds the user get desired output.

gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono).

Gemvid is a monitoring system that quantifies overall free movements of rodents without any markers, using a commercially available CCTV and a newly designed motion detection software developed on a GNU/Linux-operating computer.

GO4J is a set of API to manipulate local GO vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids.

GeneCite permits users to specify sophisticated sets of queries and generates a table of the number of citations found for each query. The table can be presented as a web page or in standard spreadsheet format.

GeneGnome will allow users to build, in the GUI, nodular models of linked cellular enzyme networks in a GNOME environment with the goal of using the underlying calculational engine linked to the GUI to help make testable predictions in real cells.

Gene Picker is a tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This woul

Gints aims at the simulation of regulation networks.

GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work.

The Genetic Data analysis Library (GDL) is a dynamic library consisting of a large panel of low-level functions in C for performing various statistical analyses of data from quantitative genomics and genetics.

This Program has a core PHP function that generates venn diagrams, with user input as gene lists, through html forms using java script

GenLux is a project focused on the structural organisation of genes, e.g. promoters, splice-sites, etc. To elucidate certain aspects and verify data, modules (written in PERL, Java, etc) are released and put together in a "construction-set"-fashion.

This this the codebase for the Genopolis Gene Expression database (http://www.genopolis.it). It is presented here for futher puplic development or as a resource for similar projects.

Genpak is a set of simple tools for manipulation of nucleic and protein sequences, written in ANSI C. The programs are supposed to be small, efective, use the Unix pipe/redirect and have a GUI via WWW/CGI.

Browsing and Annotation of complete or incomplete genomes. Live GUI-manipiulation of the underlying database (with write access).

Gene Function Identification Tool (GFIT) for post-sequencing analyses. UNIX+PERL enables us to query multi-entries and focus on what we want to see.

Ghemical is a molecular modelling package. The graphical user interface is built on GTK2. Both quantum-mechanical and forcefield-based methods are supported, and it is also possible to add new methods.

Produce Gene Set Enrichment Analysis (Broad Institute - GSEA) compatible hierarchical GO based gene sets (MSigDB format) using GO project term relationships and gene/GO term association data from multiple data sources.

<< Not released any file yet >> GOR-family algorithms for protein secondary structure prediction.

Graphical User Interface for NCBI Stand alone BLAST. This is aimed to Windows users sice NCBI BLAST is only command line in Windows. But can be also used in UNIX. Requires Python, wxPython and BioPython.

under development

A novel protein function prediction technique that helps identify the function of a protein when there are no known similar alignments. Calculations are performed without the need for computationally expensive alignment algorithms or databases.

<< Not released any file yet >> Spatial, 3D distribution of the hydrophobicity around the protein molecule, (M)olecular (H)ydrophobicity (P)otential (MHP) concept, intra- and inter-molecular interaction.

The program calculates a hydrophobicity plot. Several sets of parameters can be used. (under construction)

I, Librarian is a tool to build a web-based annotated library of scientific PDF articles. It is suitable for individuals as well as for small collaborative groups, like science labs or departments.

The IDEAs platform is an integration tool for querying and visualising Interactions, Domains, Experimental results and Annotations. It is intended for visualising omics data in context of a network of relationships between biological objects of interest.

Ishmael is a standalone browser for the BioMOBY Biological Web Services system. Source is in CVS.

ISPyB Pocket Sample bridges the gap between the Crystalization information system (PIMS, ...) and the Information System for Protein crYstallography Beamlines : ISPyB. It keeps track of samples via datamatrix codes, ...

iVUN was designed to investigate and analyze system models of biochemical reaction networks as well as the attributes describing the systems behavior. These include outputs, samples of potential parameters, and dynamic samples of fluxes and states.

Java based Molecular Biologist's Workbench

Jannotatix is a java-based Sequence and Annotation viewer. It's main purpose currently is to run different motif discovery programs on the sequences, supply the correct parameters and convert the results back to gff-format.

A generic framework that could help research groups to design, accesss, search, share, and exchange bio-data. This project trys achieve this goal to help bio-data integration and management for small/middle sized research groups in avoid of purchasing exp

Amaanova analysis in Java is intended to write the amaanova package in Java with interface to R. More bio-statitical module will be ported in this way.

Comparative Analysis and Search Tool for prokaryotic genomes. The JCoast package provides a API and GUI that makes use of the standardised genome processing and storage system, GenDB.

JDesigner is a tool that allows users to visually design biochemical networks. In addition JDesigner will output standard scripts such as SBML and Jarnac script. JDesigner is also SBW compliant.

A java program for protein structure alignment and visualization.

[This project serves as a placeholder that meets all the projects (present and future) developed by Marek KochaÅ?czyk in one place.]

<< Not released any file yet >> An improvement of GOR-family algorithms for protein secondary structure prediction (LINK1, LINK2 and LINK+ methods). Based on GORx library.

This project aims to develop programs to calculate and use the log-likelihood for the pattern of gaps (LOLIPOG) in a multiple sequence alignment (MSA). Currently, only a Perl package, FA_LOLIPOG_P, is available at FTP repository.

The purpose of this project is two-fold. First of all, we would like to provide the average researcher with top-notch bioinformatics support. Second, we aim to provide a forum for bioinformaticians to distribute their work in a readily available form

Phylogenetic analysis tools for distance matrix based clustering and comparison of trees.

Mavric is both a library of phylogeny manipulation routines and a graphical interface for phylogenetic tree visualization and editing.

Bioinformatics tools and lab admistrations tools developed by Tinghua H. at MBAB lab.

The software is to handle the base calling of the melting curve SNP genotyping technique. It aims to faciltate the practical use of this genotyping technology for clinical genetic tests.

Microbial Diagnsotic Array Workstation (MDAW) is a webserver designed for manging, sharing and analysing diagnostic array data. This is a free resource which can be accessed at http://www.arraydb.org

We describe an open source library written in the R programming language for Medline literature data mining.

DNA melting simulator based on the algorithms of Poland, Scheraga, Fixman and Friere. Developed by Blake et al since 1980. More recent porting work done by Bizzaro.

This project is for developing the software tools used to create and maintain <b><a href="http://MetaDatabase.Org">MetaBase</a></b>, the database of biological databases. The use of Perl MediaWiki API is demonstrated.

In Contrast to low-level Petri Nets (Place/Transition nets), Coloured Petri nets (CPN) belong to the high level nets. The idea of CPN is to overcome some limitations of low level Petri nets by adding of higher programming languages.

MetaQTL is Java package for the meta-analysis of QTL mapping experiments.

MetaQuant is a software for the automatic and accurate quantification of GC/MS based metabolome data.

Develop a GUI interface using Perl/Tk to interact with Dr. Michael Zuker's web-based MFold. Will take in a sequence, GI, or accession number, obtain the sequence from GenBank, obtain folding parameters and results list, and then download results.

Micro cs is a Tool for Managing Affymetrix Binary Files through a Java Based Graphical User Interface. Micro-CS is available as standalone tool or as a plugin for the TM4 platform allowing the management of binary affymetrix file within the TM4.

Featuring a user-friendly graphic interface, Microarray Я US is an R-based program that seamlessly integrates functions from over a dozen or so most-widely used Bioconductor packages to offer researchers a streamlined workflow to perform routine microarr

Human microcirculation is critically affected by many disease states. Some of the changes can be visualized by side-stream dark field (SDF) imaging technology. Few reliable tools exists to analyze image data created by SDF imaging. Purpose of the gr

Bioinformatics software has progressed a great deal from c++ code running on unix systems to user-friendly GUI based workbenches and visual tools. MobBioTools is a logical step forward towards bringing essential bioinformatics functionality to your mobile

Multiplatform Molecular Visualization Program

ProteinExplorer.Org (PE) makes slides of rotatable macromolecular structure views (MolSlides.Org). (PE) works on-line or off-line (from a downloaded copy) except for saving MolSlides. This project will facilitate saving MolSlides in more situations

Development of a library and tools for object-oriented programming in Objective-C for macromolecular structure analysis. A Smalltalk-like interpreted scripting language gives access to all objects.

Msatfinder is a simple Perl script that detects perfect microsatellite repeats (1-6 bp) in nucleic acid or protein sequences. Longer motif lengths can be detected if desired, and a variety of output files suitable for further processing are generated.

MuGeN is a package for interactively exploring multiple annotated genomes simultaneously, possibly mixed with computational analysis results. Map information can be loaded from various sources, and resulting images can be exported in different formats.

A multi-threaded standalone (no web interface needed) Java BLAST client. It can run BLAST similarity searches based on input sequence(s) or the Request IDs given out by NCBI's QBLAST in both batch and multi-threaded modes.

Simple Windows GUI program to generate mutagenesis primer by inputting sequence, amino acid number, and letter of amino acid you want to mutate to. Also customize scoring scheme to make the primer fit your own need.

The goal of this project is to develop a web-based user-friendly bioinformatics workstation where scientists can store and analyze their DNA/Protein sequences. A major goal is to have "plug-in" ability for developers and scientists to add tools/features t

NeoBio is a library of bioinformatics algorithms implemented in Java. The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch and Smith & Waterman.

Netsplitter is a Mathematica software application to split biochemical networks into functional subnetworks. The download includes a user guide giving details, and a full description is available in BMC SysBio 2011 5: 25

neuroMiner aims to house and integrate the results of published microarray experiments from selected neurodegenerative diseases (Alzheimer's disease, Huntington's disease, Multiple sclerosis, and Down syndrom).

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. Simple text output is produced which can be visualised with a suite of associated Java applications, for example JCircleGraph or OligoViz.

An open source laboratory information system designed aimed at small labs who want security and data exchange in an open system based on public protocols.

The goal of the OpenNotebook project is to create a modular framework for a client side cross-platform application to assist the end user of a web-based scientific resource in storing and maintaining returned data.

Researching practical computational methods to solve the Chemical Master Equation (CME) using distrubuted/parallel algorithms executed on small PC clusters (10 processors).

A java library for protein structure analysis

PaMSA is a parallel algorithm for global multiple sequence alignment of proteins

Is a parallel distributed framework for the design of oligonucleotides suitable for microarrays.

PartiGene is an integrated sequence analysis suite consisting of a set of scripts; trace2dbEST, PartiGene.pl, prot4EST, annot8r and wwwPartiGene which process and organise EST data within a genomic context and facilitate large scale analysis.

PIPS is a software developed intending to identify Putative Pathogenicity Islands in pathogenic bacteria integrating the prediction of several algorithms. Later Versions of PIPS are planned that will turn the application faster and more accurate.

Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances. Patristic provides different graphic views of the results.

PCalc is a software designed to help molecular biologists in routine procedures of concentrations calculus in PCR, like calculus of primer concentration, calculus of annealing temperature (DNA/DNA and DNA/PNA), MW primer calculation and mass units convers

pcb2png is a small utility that converts phosphoimager pcb/img files to png format

PDBH aims to develop a searchable database of rasmol scripts, designed to visually integrate data in the PDB with data from other sources. Curently we maintain a set of scripts which DEFINE, color and annotate PDB entries with their SCOP domain definition

User submits a protein sequence, and retrieves the positions which are well-conserved through several PSI-BLAST iterations. Conservation is parameterized by use of aa alphabet, use of priors, and voting scheme.

Extension of perl OO system influenced by Frames / ontology research

Phenotyper is a system for collecting phenotyping data especially for plant breeding and science using handhelds for data input and web tools both for creating schemes for the user interface and managing result data.

Phoenix is a C++ parser for EMBL-Bank flat files.

PHP Labware develops PHP software like the LabStoRe LIMS and OrderSys ordering/purchase systems for day-to-day usage by research groups/laboratories

a web interface to manage biological samples (species, samples, DNA sequences, PCRs)

phpPhylotree is a web application that is able to draw phylogenetic trees. it produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.

Poly is a program for the quantitative analysis of simple sequence repeats (SSRs) in DNA.

polyxmass is a software suite for (bio)polymer mass spectrometry that is Free Software developed on GNU/Linux. It allows the definition of polymer chemistries and the simulation/analysis of mass spectrometric data obtained on (bio)polymers.

Population genetic software: individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.

PORTRAIT (acronym for Prediction of transcriptomic ncRNA by ab initio methods) is an algorithm for identifying non-coding RNAs on a transcriptome context.

PREP is a Perl script designed to allow the usage of regexps within searches of Pubmed. PREP allows for the easy retrieval of Pubmed records that contain terms that can be more easy matched by a textual pattern than a traditional keyword query.

Tools for aligning PCR primers or similar short DNA sequences against genomic sequence. Many options for constraining acceptable alignments and input/output formats. Automatically optimizes the sequence search stategy for search parameters.

PrimerPy is a free GUI tool for optimal QPCR primer design, using "Primer3" as a backend engine. The design's been validated by laboratory experiences; applicable to conventional PCR too.

A web-based program that automates design of mutagenic PCR primers for site-directed mutagenesis.

PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison

User friendly PDB (Protein Data Bank) file editor with graphic user interface Tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files

PyMsXML is a python script for converting vendor specific mass spectrometry data files from their proprietary binary format, to either of the emerging XML file formats for mass spectra: mzXML or mzData.

A Python-based tool for accurate analysis of qPCR data using global fitting

RDFBuilder is a Java library that allows performing SPARQL queries to ArrayExpress microarray repositories. This library can be freely downloaded and used in other software projects.

Automated molecular palaeontology of repetitive DNA elements. Input: RepeatMasker annotation. Outputs: 1) Defragmentation of elements. 2) Inference of nesting structure. 3) Estimates of the ages of LTR-elements. 4) Multiply aligned element sequences.

REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies

A bioinformatics data-updater. This small PHP code would retrieve the current release files from the premier databases, parse it, and then list only the salient features all in one single go.

The Scriptome is a set of tools and protocols that helps biologists format, merge, and filter files. While designed for non-programmers, it can also help beginners learn Perl if they choose, and serve as a "cookbook" for experienced programmers.

SEARCHPATTOOL is a program for analyzing DNA sequences in order to discover patterns or motifs for binding sites. It is based on exhaustive algorithm and is dedicated to prokaryotic species or genes with small promoter regions.

seKs will be an easy to use sequence editor, running in the KDE3 environment. It will provide a nice GUI to edit, analyze and anotate DNA, RNA and protein sequences. Status: heavy development, nothing for the public yet Dependencies: QT3, boost

SeqDoC (Sequence Difference of Chromatograms) aligns and performs a subtractive comparison of two ABI DNA sequence chromoatograms. The subtracted profile is processed to highlight differences characteristic of single base changes.

Accepts a DNA sequence and a set of primer sequences and returns a textual figure showing the annealing positions of the primers, restriction cut sites, and protein translations. Nested JavaScript code makes the figure interactive.

The Sequence Manipulation Suite 1 is a collection of web-based programs for analyzing and formatting DNA and protein sequences.

The Sequence Manipulation Suite 2 is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, and for teaching purposes.

Sequence Studio main package provides classes and interfaces for various kinds of sequence alignment

SEQUEROME is a web-based Sequence profiling tool that provides a unique feature of completely profiling a BLAST report within a single browser interface by providing simplified access to web-distributed resources for protein and nucleic acid analysis.

SeWeR is an very popular integrated, customizable, platform-independent web interface to bioinformatics services available over WWW.

Sight, a java-based package that provides a user-friendly interface to create and connect agents for automatic genomic data mining for individual purposes. No programming skills are required, but very strong support for programmers is implemented.

This is the Bioinformatics.org administration group.

SiteFind is a molecular biology tool that enables a scientist performing site-directed mutagenesis to simultaneously introduce a restriction site as a maker for successful mutagenesis.

The Samuel Lunenfeld Research Institute (SLRI) Bioinformatics Toolkit is a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function. Visit our project home page for more information.

A Smith Waterman sequence alignment algorithm implemented to run on GreenTea P2P decentralized distributed network computing platform

SNA is a Mathematica toolbox for stoichiometric network analysis. Among other things, it supports flux balance analysis and the enumeration of the elementary vectors of the flux and the conversion cone.

Design primers for Snapshot to do allele specific analysis

SNPsel generates allelic sequences by combining a single sequence with its SNPs, used as input for TFBS prediction programs (MULAN, MAPPER, MatInspector) to find TFBS affected by SNPs on both (allelic) sequences.

A n illustrative example for the current situation in immunological research is the case of cytokine networks. Cytokines are small protein or glycoprotein messenger molecules that convey information from one cell to another. Various aspects of the immune

The idea is to combine a 'wiki' system with SQL queries, allowing data driven pages to be constructed by the user. The most important aspects are results formatting and parameter passing between data driven pages. The major hurdle is security.

The Short Sequence Assembly by K-mer search and 3' read Extension is a genomics application for aggressively assembling millions of short (25-36bp) nucleotide sequences.

Strainer is a multi-platform visualization tool for metagenomics data. It allows the user to easily browse the variation present in assembled shotgun sequence data from non-clonal samples.

The computer program STRAP supports the analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA- sequence and residue annotation.

OSPRAI is the Open-source SPR Analysis and Integration software. This project develops interactive command-line tools for accessing, viewing, analyzing, and saving sensorgram from various surface plasmon resonance instruments including microarray imagers

The project is to develop an efficient and useful clustering algorithm. The project currently includes computer code written in Matlab for performing singular value decomposition followed by fuzzy K-means clustering on adjacency matrices.

Free and open source software implementation of t-CWT for MATLAB and GNU Octave. t-CWT is a method for multivariate assessment of event-related potentials (ERP) based on the continuous wavelet transform (CWT) and Student's t-test.

A Java taxonomy browser GUI designed to run as a plugin or standalone. Currently works with the NCBI taxonomy.

TeXMed is a simple web-interface to query NCBI PubMed to export references in bitex format.

Text2Knowledge is aiming to provide text mining tools for medical texts. It utilizes natural language processing techniques to extract patterns for specific domains...

TfReg implements the Peyrard-Bishop model for DNA and RNA duplexes. You can use it to calculate melting temperatures by entering the strength of the hydrogen bond or to obtain sequence-dependent opening profiles.

Imagine that every web server was a generic CGI calculator, and you could compile code to 'run on the web'...

The Tandem Repeat Occurrence Locator is a light weight SSR finder based on a slight modification of the Aho-Corasick algorithm.

The Dynamic Local Storage Tool is a simple PHP/Apache/MySQL application that downloads and maintains local databases containing relational UniGene keys for selected species.

[structural proteomics | JavaWebStart, OpenGL] Applies methods of defining conformational subspace for early-stage protein folding/structural similarity estimation by means of geometrical parameters of the polypeptide chain (see Bioinformatics papers)

VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution. It includes a variety of sequence and structure analysis packages.It is an Open source product released under G

The W-curve is a numerical mapping, pattern recognition algorithm that shows significant potential for achieving visual consensus for the class of long repetitive sequences found in long genomic strings.

The name (without the a?s) stands for ?Web Services for Bioinformatics?. Wasabi is both an initiative to refactor popular informatics utilities as Web services and a piping infrastructure enabling those services to be linked to solve complex problems.

WAX is general framework for tying together XML based applications on the web using RDF. Some code in CVS.

WinBLAST is a Windows graphical front-end for NCBI BLAST. It is written completely in C#, utilizing Microsoft?s latest .NET framework. WinBLAST will run on any Windows machine that supports Microsoft .NET framework. WinBLAST has an intuitive user inter

Simple, declarative, bijective inter-conversion between MATLAB structured variables and XML strings. A specialized markup language, MbML, was defined to support string representation of any MATLAB variable: any XML --> MbML <--> MATLAB

Yet Another Microbial/Metagenomic Annotation Pipeline/Program is a Perl application created for the NERC Microbial Metagenomics programme. It is designed to be a user-friendly way for Bio-Linux users to run a selection of first-pass annotation tools upon

Yinteraction is a software for predicting genetic protein-protein interactions and pathways in bakery yeast, Saccharomyces cerevisiae. It uses two databases derived of the BioGrid and the SGD databases.

YNGS assembles pair-end fastq data by starting from a seed and elongates the string loop by loop. Matching fastq fragments can be counted for each position and can be displayed for each loop.

The software displays a 3D model of DNA-Nucleosome interactions of experimental validated Nucleosome positions of the bakery yeast Saccharomyces cerevisiae. It displays the nucleosome core particle H3,H4,H2A,H2B and the 146 bp long DNA fragment.