Flashcards: Bioinformatics

Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences.

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects.

Folding@home (FAH or F@h) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics.

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

PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities.

Medical Subject Headings (MeSH) is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it serves as a thesaurus that facilitates searching.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data.

The NCBI houses a series of databases relevant to biotechnology and biomedicine and an important resource for bioinformatics tools and services.

Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker laboratory at the University of Washington.

A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.

The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze.

PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function.

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships.

WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes.

The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”.

MetaboMiner is a tool which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D-NMR spectra.

MitoMap is a real time haplotyping protocol that analyzes pathogenic variants that cause several mitochondrial diseases.

ShiftX (Shifts from X-ray structures) is a freely available web server for rapidly calculating protein chemical shifts from protein X-ray (or NMR) coordinates.

Volume, Area, Dihedral Angle Reporter (VADAR) is a freely available protein structure validation web server that was developed as a collaboration between Dr.

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

The prize was established by the International Society for Computational Biology (ISCB) in memory of G.

The Pathogen-Host Interaction database (PHI-base) contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions.

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

bioSearch is a web application developed to manage marine biodiversity data from Indian waters.

Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species.

The European Conference on Computational Biology (ECCB) is a scientific meeting on the subjects of bioinformatics and computational biology.

FSA is a multiple sequence alignment program for aligning many proteins or RNAs or long genomic DNA sequences.

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

In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA.

Gemini Somatics is a biotechnology company located in Riverside, Oregon, working primarily in the field of synthetic somatology, which is an emerging science developed by Dr Edward Darmos.

GenePattern is a freely available computational biology open-source software package developed at the Broad Institute of MIT and Harvard for the analysis of genomic data.

Gene Designer is a free bioinformatics software package.

Genomatix GmbH is a computational biology company headquartered in Munich, Germany, with a seat of business in Ann Arbor, Michigan, U.

The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by High-throughput sequencing, which are typically less than 1,000 base pairs in length.

WormBook is an open access, comprehensive collection of original, peer-reviewed chapters covering topics related to the biology of the nematode worm Caenorhabditis elegans (C. elegans).

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

Research in Computational Molecular Biology (RECOMB) is an annual academic conference on the subjects of bioinformatics and computational biology.

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

In bioinformatics the PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products.

In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer.

The Giant Virus Finder is a free bioinformatics software for finding giant viruses in metagenomes.

OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence.

The Basel Computational Biology Conference (stylized as [BC]2) is a scientific meeting on the subjects of bioinformatics and computational biology.

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language.

is a bioinformatics software, the name is an abbreviation for phylogenetic investigation of communities by reconstructionof unobserved states.

In epidemiology, the attack rate is the biostatistical measure of frequency of morbidity, or speed of spread, in an at risk population.

There are two workflows that are of interest to scientists that use Minimotif Miner 1) Entering any query protein into Minimotif Miner returns a table with a list of minimotif sequence and functions that have a sequence pattern match with the protein query sequence.

The National Center for Genome Resources (NCGR) is a nonprofit research organization in Santa Fe, New Mexico founded in 1994 focusing on life sciences research, bioinformatics technologies, and leading-edge molecular data production including sequencing and gene expression.

neXtProt is an on-line knowledge platform on human proteins.

NextBio is a privately owned software company that provides a platform for drug companies and life science researchers to search, discover, and share knowledge across public and proprietary data.

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

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

CAMERA, or the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis, is an online cloud computing service that provides hosted software tools and a high-performance computing infrastructure for the analysis of metagenomic data.

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

In molecular biology and bioinformatics, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population.

ABCdb is a biological database for the ATP-binding Cassette (ABC) transporters encoded by completely sequenced archaeal and (eu)bacterial genomes.

Applied Maths NV is a bioinformatics company, headquartered in Sint-Martens-Latem, Belgium, developing software for the biosciences.

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

CAZy is a database of Carbohydrate-Active enZYmes (CAZymes).

CLC bio is a bioinformatics software company headquartered in Aarhus, Denmark, and with offices in Cambridge, Massachusetts, Tokyo, Taipei and Delhi.

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 caGrid computer network and software supported the cancer Biomedical Informatics Grid (caBIG) initiative of the National Cancer Institute of the US National Institutes of Health.

Canadian Bioinformatics Workshops (CBW) are a series of advanced training workshops in bioinformatics, founded in 1999 in response to an identified need for a skilled bioinformatics workforce in Canada.

Consed is a program for viewing, editing, and finishing DNA sequence assemblies.

The ISCB Africa ASBCB Conference on Bioinformatics is a biennial academic conference on the subjects of bioinformatics and computational biology, organized by the African Society for Bioinformatics and Computational Biology (ASBCB).

The Integrated Microbial Genomes (IMG) system is a genome browsing and annotation platform developed by the U.

Intelligent Systems for Molecular Biology (ISMB) is an annual academic conference on the subjects of bioinformatics and computational biology organised by the International Society for Computational Biology (ISCB).

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