|
Staden Package
The Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a BSD 3-clause license. Package components The Staden package consists of several different programs. The main components are: * pregap4 – base calling with Phred, end clipping, and vector trimming * trev – trace viewing and editing * gap4 – sequence assembly, contig editing, and finishing * gap5 – assembly visualising, editing, and finishing of NGS data * Spin – DNA and protein sequence analysis History The Staden Package was developed by Rodger Staden's group at the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England, since 1977. The package was available free to academic users, with 2,500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development ended. The package was converted to open-source in 2004, and several new versions have been rele ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C (programming Language)
C (''pronounced like the letter c'') is a General-purpose language, general-purpose computer programming language. It was created in the 1970s by Dennis Ritchie, and remains very widely used and influential. By design, C's features cleanly reflect the capabilities of the targeted CPUs. It has found lasting use in operating systems, device drivers, protocol stacks, though decreasingly for application software. C is commonly used on computer architectures that range from the largest supercomputers to the smallest microcontrollers and embedded systems. A successor to the programming language B (programming language), B, C was originally developed at Bell Labs by Ritchie between 1972 and 1973 to construct utilities running on Unix. It was applied to re-implementing the kernel of the Unix operating system. During the 1980s, C gradually gained popularity. It has become one of the measuring programming language popularity, most widely used programming languages, with C compilers avail ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phred Base Calling
Phred is a computer program for base calling, that is to say, identifying a nucleobase sequence from fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, Phred produced significantly fewer errors in the data sets examined than other methods, averaging 40–50% fewer errors. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Background The fluorescent-dye DNA sequencing is a molecular biology technique that involves labeling single-strand DNA sequences of varied length with 4 fluorescent dyes (corresponding to 4 different bases used in DNA) and subsequently separating the DNA sequences by "slab gel"- or capillary-electrophoresis method (see DNA Sequencing). The electrophoresis run is monitored by a CCD on the DNA sequencer and this produces a time "trace" data (or "chr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vector NTI
Vector NTI was a commercial bioinformatics software package used by many life scientists in the early 2000s to work, among other things, with nucleic acids and proteins '' in silico''. It allowed researchers to, for example, plan a DNA cloning experiment on the computer before actually performing it in the lab. It was originally created by InforMax Inc, North Bethesda, MD in 1993 and versions in the early 2000s were well reviewed at the time. However, in 2008 it was locked and turned into a commercial software after 2008 which created problems for locked in users who were forced to buy the software to continue accessing their data on newer computers. What was previously a single software package was subsequently split into Vector NTI Express, Advanced, and Express Designer. Vector NTI was discontinued by its corporate parent Thermo Fisher at the end of 2019 and support ceased a year later. Features * create, annotate, analyse, and share DNA/protein sequences * perform and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UGENE
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2. UGENE helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g., a lab database). UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE provides a graphical user interface (GUI) for the pre-built tools so biologists with no computer programming skills can access those tools more easily. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MacVector
MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by Molecular biology, molecular biologists to help analyze, design, research and document their experiments in the laboratory. MacVector 18.1 is a Universal binary, Universal Binary capable of running on Intel and Apple Silicon Macs. Features MacVector is a collection of sequence analysis algorithms linked to various sequence editors, including a single sequence editor, a multiple sequence alignment editor and a contig editor. MacVector tries to use a minimum of windows and steps to access all the functionality. Functions include: * Sequence alignment (ClustalW, MUSCLE (alignment software), Muscle and T-COFFEE, T-Coffee) and editing. * Subsequence search and open reading frames (ORFs) analysis. * Phylogenetic tree construction UPGMA, Neighbour joining with bootstrapping and consensus trees * Online Database searching - Search public databases at the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CodonCode Aligner
CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. Features Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built-in algorithms, mutation detection, including detection of heterozygous single-nucleotide polymorphism, analysis of heterozygous insertions and deletions, start online BLAST searches, restriction analysis (find and view restriction cut sites), trace sharpening, and support for Phred, Phrap, ClustalW, and MUSCLE. History The first beta version of CodonCode Aligner was released in April 2003, followed by the first full version in June 2003. Major upgrades were released in 2003, 2004, 2005, 2006, 2007, and 2008. In April 2009, CodonCode Aligner had been cited in more than 400 scientific publi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Consed
Consed is a program for viewing, editing, and finishing DNA sequence assemblies. Originally developed for sequence assemblies created with phrap, recent versions also support other sequence assembly programs like Newbler. History Consed was originally developed as a contig editing and finishing tool for large-scale cosmid shotgun sequencing in the Human Genome Project. At genome sequencing centers, Consed was used to check assemblies generated by phrap, solve assembly problems like those caused by highly identical repeats, and finishing tasks like primer picking and gap closure. Development of Consed has continued after the completion of the Human Genome Project. Current Consed versions support very large projects with millions of reads, enabling the use with newer sequencing methods like 454 sequencing and Solexa Illumina, Inc. is an American biotechnology company, headquartered in San Diego, California. Incorporated on April 1, 1998, Illumina develops, manufactures, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phrap
Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package. History Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the Human Genome Project. Phrap has been widely used for many different sequence assembly projects, including bacterial genome assemblies and EST assemblies. Phrap was written as a command line program for easy integration into automated data workflows in genome sequencing centers. For users who want to use Phrap from a graphical interface, the commercial programs MacVector (for Mac OS X only) and CodonCode Aligner (for Mac OS X and Microsoft Windows) are available. Methods A detailed (albeit partially outdated) description of the Phrap algorithms can be found in thPhrap documentation A recurring thread within the Phrap algorithms is the use of Phred quality scores. Phrap used quality scores to mitigate a problem that other assembly progra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Compiler
Twist Bioscience is a public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products for customers in a wide range of industries. Twist was founded in 2013 by Emily Leproust, Bill Banyai, and Bill Peck. The company was represented by Leproust at a March 2021 tabletop exercise at the Munich Security Conference simulating an outbreak of weaponized monkeypox Monkeypox (also called mpox by the WHO) is an infectious viral disease that can occur in humans and some other animals. Symptoms include fever, swollen lymph nodes, and a rash that forms blisters and then crusts over. The time from exposure t .... References {{Reflist Companies based in South San Francisco, California American companies established in 2013 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Laboratory Of Molecular Biology
The Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) is a research institute in Cambridge, England, involved in the revolution in molecular biology which occurred in the 1950–60s. Since then it has remained a major medical research laboratory at the forefront of scientific discovery, dedicated to improving the understanding of key biological processes at atomic, molecular and cellular levels using multidisciplinary methods, with a focus on using this knowledge to address key issues in human health. A new replacement building constructed close by to the original site on the Cambridge Biomedical Campus was opened by Her Majesty the Queen in May 2013. The road outside the new building is named Francis Crick Avenue after the 1962 joint Nobel Prize winner and LMB alumnus, who co-discovered the helical structure of DNA in 1953. History Origins: 1947-61 Max Perutz, following undergraduate training in organic chemistry, left Austria in 1936 and came to the Universi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Medical Research Council (United Kingdom)
The Medical Research Council (MRC) is responsible for co-coordinating and funding medical research in the United Kingdom. It is part of United Kingdom Research and Innovation (UKRI), which came into operation 1 April 2018, and brings together the UK's seven research councils, Innovate UK and Research England. UK Research and Innovation is answerable to, although politically independent from, the Department for Business, Energy and Industrial Strategy. The MRC focuses on high-impact research and has provided the financial support and scientific expertise behind a number of medical breakthroughs, including the development of penicillin and the discovery of the structure of DNA. Research funded by the MRC has produced 32 Nobel Prize winners to date. History The MRC was founded as the Medical Research Committee and Advisory Council in 1913, with its prime role being the distribution of medical research funds under the terms of the National Insurance Act 1911. This was a consequen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
