Flashcards: Bioinformatics software

Foldit is an online puzzle video game about protein folding.

Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists.

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome.

RAPTOR is protein threading software used for protein structure prediction.

taveRNA is a software suite for RNA/DNA secondary structure.

UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

UTOPIA (User-friendly Tools for OPerating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data.

WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields.

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

Omixon is a global biotechnology company that commercializes disruptive innovations specializing in targeted applications for Next Generation Sequencing (NGS).

Mega2, the Manipulation Environment for Genetic Analysis, allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages.

BioJS is an open source project for bioinformatics data on the web.

PLINK is a free, commonly used, open-source whole genome association analysis toolset designed by Shaun Purcell.

PSIPRED (Psi-blast based secondary structure prediction) is a technique used to investigate protein structure.

Vector NTI is a commercial bioinformatics software package used by many life scientists to work, among other things, with nucleic acids and proteins in silico .

Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees.

SplitsTree is a popular program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees.

AstridBio Inc. is a privately held bioinformatics company with offices in Canada, Luxembourg and Hungary.

Sirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center.

BioJava is an open source project dedicated to providing Java tools for processing biological data.

Jmol is an open-source Java tool for molecular modelling chemical structures in 3D.

FlyExpress is a free database that collects the expression patterns of Drosophila melanogaster in embryogenesis via a series of images submitted from BDGP, Fly-FISH and publications from other researchers, containing over 100,000 images of over 4,000 genes.

I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences.

BioNumerics is a suite of bioinformatics software applications developed by the company Applied Maths NV.

BioPHP is a collection of open source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools.

BioRuby is a collection of Open Source Ruby code, comprising classes for computation molecular biology and bioinformatics.

Biskit is an open source software package written in Python.

In bioinformatics GENSCAN is a program to identify complete gene structures in genomic DNA.

GESS is a computer program for analyzing gene expression data obtained from microarrays.

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease.

GenGIS merges geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment.

Gene Designer is a free bioinformatics software package.

GenomeSpace is an environment for genomics software tools and applications.

LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data.

XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars.

YASS is a free software, pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences.

ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses.

AlleleID designs oligos for strain differentiation and taxa specific assays.

AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow.

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.

esyN (Easy Networks) is an open source bioinformatics web-tool for visualizing, building and analysing molecular interaction networks.

The Biopython Project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers.

DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB).

DNASTAR is a global bioinformatics software company incorporated in 1984 that is headquartered in Madison, Wisconsin.

PrimerPlex designs oligos for standard multiplex PCR assays and for bead-based suspension array systems such as BioPlex-200 and Luminex 100/200 based on xMAP technology.

Primer Premier software combines design of primers for various PCR applications under one common platform.

Stemloc is a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair stochastic context-free grammars.

IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data.

The Budapest Reference Connectome computes the frequently appearing anatomical brain connections of 418 healthy subjects.

Mesquite is a software package primarily designed for phylogenetic analyses.

Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are web-based services for protein structure prediction that are free for non-commercial use.

In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.

UGENE is free open-source bioinformatics software.

NoeClone is a bioinformatics software which can run in multiple operating systems (Windows, Mac OS, Unix/Linux) with the same interface.

FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J.

Orange is a free software machine learning and data mining package (written in Python).

eMovie is a plug-in for PyMOL that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of traditional movies.

In bioinformatics, MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences.

MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets.

SEQUEST is a tandem mass spectrometry data analysis program used for protein identification.

Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences.

Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees.

ArrayTrack is a multi-purpose bioinformatics tool primarily used for microarray data management, analysis, and interpretation.

CS-BLAST (Context-Specific BLAST) is a protein sequence search tools that extends BLAST (Basic Local Alignment Search Tool), (Basic Local Alignment Search Tool) by context-specific mutation probabilities.

The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics.

HHsearch is an open-source software program for protein sequence searching that is part of the free HH-suite software package.

HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy.

Handel is a suite of programs for multiple sequence alignment.

Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.

Integromics is a global bioinformatics company headquartered in Granada, Spain, with a second office in Madrid and subsidiaries in the US and UK and distributors in 10 countries.