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UGENE
UGENE is computer software for bioinformatics. It helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. 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 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. The data can be stored both locally and on shared/networked storage. The graphical user interface (GUI) provides access to pre-built tools so users with no computer programming experience can access those tools easily. UGENE also has a command-line interface to execute Workflows. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MUSCLE (alignment Software)
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is Software license, licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in ''Nucleic Acids Research'', introduced the sequence alignment algorithm. The second paper, published in ''BMC Bioinformatics'', presented more technical details. MUSCLE up to version 3 uses a progressive-refinement method. Since version 5 it uses a hidden Markov model similar to ProbCons. History Robert C. Edgar Edgar graduated in 1982 from University College London, BSc in Physics, PhD in Particle physics. He pursued software development post-graduation and founded his own company, Parity Software, in 1988. In 2001, he began working with coding algorithms after attending a seminar at the University of California Berkley. From 2001-present day Edgar has contributed to or been the sole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibiti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free And Open-source Software
Free and open-source software (FOSS) is software available under a license that grants users the right to use, modify, and distribute the software modified or not to everyone free of charge. FOSS is an inclusive umbrella term encompassing free software and open-source software. The rights guaranteed by FOSS originate from the "Four Essential Freedoms" of '' The Free Software Definition'' and the criteria of '' The Open Source Definition''. All FOSS can have publicly available source code, but not all source-available software is FOSS. FOSS is the opposite of proprietary software, which is licensed restrictively or has undisclosed source code. The historical precursor to FOSS was the hobbyist and academic public domain software ecosystem of the 1960s to 1980s. Free and open-source operating systems such as Linux distributions and descendants of BSD are widely used, powering millions of servers, desktops, smartphones, and other devices. Free-software licenses and open-so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graphical User Interface
A graphical user interface, or GUI, is a form of user interface that allows user (computing), users to human–computer interaction, interact with electronic devices through Graphics, graphical icon (computing), icons and visual indicators such as secondary notation. In many applications, GUIs are used instead of text-based user interface, text-based UIs, which are based on typed command labels or text navigation. GUIs were introduced in reaction to the perceived steep learning curve of command-line interfaces (CLIs), which require commands to be typed on a computer keyboard. The actions in a GUI are usually performed through direct manipulation interface, direct manipulation of the graphical elements. Beyond computers, GUIs are used in many handheld mobile devices such as MP3 players, portable media players, gaming devices, smartphones and smaller household, office and Distributed control system, industrial controls. The term ''GUI'' tends not to be applied to other lower-displa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Programming
Computer programming or coding is the composition of sequences of instructions, called computer program, programs, that computers can follow to perform tasks. It involves designing and implementing algorithms, step-by-step specifications of procedures, by writing source code, code in one or more programming languages. Programmers typically use high-level programming languages that are more easily intelligible to humans than machine code, which is directly executed by the central processing unit. Proficient programming usually requires expertise in several different subjects, including knowledge of the Domain (software engineering), application domain, details of programming languages and generic code library (computing), libraries, specialized algorithms, and Logic#Formal logic, formal logic. Auxiliary tasks accompanying and related to programming include Requirements analysis, analyzing requirements, Software testing, testing, debugging (investigating and fixing problems), imple ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command-line Interface
A command-line interface (CLI) is a means of interacting with software via command (computing), commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user-friendly alternative to the non-interactive mode available with punched cards. For a long time, a CLI was the most common interface for software, but today a graphical user interface (GUI) is more common. Nonetheless, many programs such as operating system and software development utility software, utilities still provide CLI. A CLI enables automation, automating computer program, programs since commands can be stored in a scripting language, script computer file, file that can be used repeatedly. A script allows its contained commands to be executed as group; as a program; as a command. A CLI is made possible by command-line interpreters or command-line processors, which are programs that execute input commands. Alternatives to a CLI ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graphics Processing Unit
A graphics processing unit (GPU) is a specialized electronic circuit designed for digital image processing and to accelerate computer graphics, being present either as a discrete video card or embedded on motherboards, mobile phones, personal computers, workstations, and game consoles. GPUs were later found to be useful for non-graphic calculations involving embarrassingly parallel problems due to their parallel structure. The ability of GPUs to rapidly perform vast numbers of calculations has led to their adoption in diverse fields including artificial intelligence (AI) where they excel at handling data-intensive and computationally demanding tasks. Other non-graphical uses include the training of neural networks and cryptocurrency mining. History 1970s Arcade system boards have used specialized graphics circuits since the 1970s. In early video game hardware, RAM for frame buffers was expensive, so video chips composited data together as the display was being scann ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multi-core Processor
A multi-core processor (MCP) is a microprocessor on a single integrated circuit (IC) with two or more separate central processing units (CPUs), called ''cores'' to emphasize their multiplicity (for example, ''dual-core'' or ''quad-core''). Each core reads and executes Instruction set, program instructions, specifically ordinary Instruction set, CPU instructions (such as add, move data, and branch). However, the MCP can run instructions on separate cores at the same time, increasing overall speed for programs that support Multithreading (computer architecture), multithreading or other parallel computing techniques. Manufacturers typically integrate the cores onto a single IC Die (integrated circuit), die, known as a ''chip multiprocessor'' (CMP), or onto multiple dies in a single Chip carrier, chip package. As of 2024, the microprocessors used in almost all new personal computers are multi-core. A multi-core processor implements multiprocessing in a single physical package. Des ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virology
Virology is the Scientific method, scientific study of biological viruses. It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host (biology), host cell (biology), cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy. The identification of the causative agent of tobacco mosaic disease (TMV) as a novel pathogen by Martinus Beijerinck (1898) is now acknowledged as being the history of virology, official beginning of the field of virology as a discipline distinct from bacteriology. He realized the source was neither a bacterial nor a fungal infection, but something completely different. Beijerinck used the word "virus" to describe the mysterious agent in his 'contagium vivum fluidum' ('contagious living fluid'). Rosalind Franklin proposed the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
