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Fast Statistical Alignment
Fast statistical alignment or FSA is a multiple sequence alignment program for aligning many proteins, RNAs, or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to more reliably identify non-homologous sequences than these other programs, although this increased accuracy comes at the cost of decreased speed. FSA is currently being used for multiple projects, including sequencing new worm genomes and analyzing ''in vivo'' transcription factor binding in flies. Input/Output This program accepts sequences in FASTA format and outputs alignments in FASTA format or Stockholm format. Algorithm The algorithm for the aligning of the input sequences has 4 core components. Pair Hidden Markov Model for generating posterior probabilities The algorithm starts first by determining posterior probabilities ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UC Berkeley
The University of California, Berkeley (UC Berkeley, Berkeley, Cal, or California) is a public university, public land-grant university, land-grant research university in Berkeley, California. Established in 1868 as the University of California, it is the state's first land-grant university and the founding campus of the University of California system. Its fourteen colleges and schools offer over 350 degree programs and enroll some 31,800 undergraduate and 13,200 graduate students. Berkeley ranks among the world's top universities. A founding member of the Association of American Universities, Berkeley hosts many leading research institutes dedicated to science, engineering, and mathematics. The university founded and maintains close relationships with three United States Department of Energy National Laboratories, national laboratories at Lawrence Berkeley National Laboratory, Berkeley, Lawrence Livermore National Laboratory, Livermore and Los Alamos National Laboratory, Los ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UW Madison
UW, U.W., ''Uw'', or uw may refer to: Universities Canada * University of Waterloo * University of Windsor * University of Winnipeg United States * University of Washington * University of Wisconsin System * University of Wisconsin–La Crosse * University of Wisconsin–Madison * University of Wisconsin–Milwaukee * University of Wyoming Other countries * University of Warsaw, Poland * University of Wuppertal, Germany * University of Würzburg, Germany Other uses * uw (digraph) * ''Uw'', the international symbol for relative humidity * Unconventional warfare * Unconventional warfare (United States) In United States military doctrine, ''unconventional warfare'' (abbreviated ''UW'') is one of the core activities of irregular warfare. Unconventional warfare is essentially support provided by the military to a foreign insurgency or resistance. ..., a US-specific definition of unconventional warfare used by its Department of Defense * '' Unia Wolnosci'' (Freedom Union), a Pol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lior Pachter
Lior Samuel Pachter is a computational biologist. He works at the California Institute of Technology, where he is the Bren Professor of Computational Biology. He has widely varied research interests including genomics, combinatorics, computational geometry, machine learning, scientific computing, and statistics.. Early life and education Pachter was born in Israel and grew up in South Africa. He earned a bachelor's degree in mathematics from the California Institute of Technology in 1994. He completed his doctorate in mathematics from the Massachusetts Institute of Technology in 1999, supervised by Bonnie Berger, with Eric Lander and Daniel Kleitman as co-advisors. Career and research Pachter was with the University of California, Berkeley faculty from 1999 to 2018 and was given the Sackler Chair in 2012. As well as for his technical contributions, Pachter is known for using new media to promote open science and for a thought experiment he posted on his blog according to which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UNIX
Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others. Initially intended for use inside the Bell System, AT&T licensed Unix to outside parties in the late 1970s, leading to a variety of both academic and commercial Unix variants from vendors including University of California, Berkeley (Berkeley Software Distribution, BSD), Microsoft (Xenix), Sun Microsystems (SunOS/Solaris (operating system), Solaris), Hewlett-Packard, HP/Hewlett Packard Enterprise, HPE (HP-UX), and IBM (IBM AIX, AIX). In the early 1990s, AT&T sold its rights in Unix to Novell, which then sold the UNIX trademark to The Open Group, an industry consortium founded in 1996. The Open Group allows the use of the mark for certified operating systems that comply with the Single UNIX Specification (SUS). Unix systems are chara ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apple Macintosh
The Mac (known as Macintosh until 1999) is a family of personal computers designed and marketed by Apple Inc. Macs are known for their ease of use and minimalist designs, and are popular among students, creative professionals, and software engineers. The current lineup includes the MacBook Air and MacBook Pro laptops, as well as the iMac, Mac Mini, Mac Studio and Mac Pro desktops. Macs run the macOS operating system. The first Mac was released in 1984, and was advertised with the highly-acclaimed "1984" ad. After a period of initial success, the Mac languished in the 1990s, until co-founder Steve Jobs returned to Apple in 1997. Jobs oversaw the release of many successful products, unveiled the modern Mac OS X, completed the 2005-06 Intel transition, and brought features from the iPhone back to the Mac. During Tim Cook's tenure as CEO, the Mac underwent a period of neglect, but was later reinvigorated with the introduction of popular high-end Macs and the ongoing Apple s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Sequence
A nucleic acid sequence is a succession of Nucleobase, bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the Directionality (molecular biology), 5' end to the 3' end. For DNA, the Sense (molecular biology), sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the Biomolecular structure#Primary structure, primary structure. The sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of an organism. Nucleic acids also have a Nucleic acid secondary structure, secondary structure and Nucleic acid tertiary structure, tertiary structure. Primary structur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MUSCLE (alignment Software)
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is 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. Algorithm The MUSCLE algorithm proceeds in three stages: the ''draft progressive'', ''improved progressive'', and ''refinement'' stage. Stage 1: Draft Progressive In this first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy. This step begins by computing the k-mer distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a progressive alignment is constructed, beginning with the creation of profiles for each leaf of the tree ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MAFFT
In bioinformatics, MAFFT (for multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version of MAFFT used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the Fast Fourier Transform. Subsequent versions of MAFFT have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and the addition of new sequences to existing alignments. See also * Sequence alignment software * Clustal Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its a ... References External links * MAFFT Online ServerMAFFT ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like the R programming language, Python, Ruby, Haskell, and Perl. Original format & overview The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number). In the original format, a sequence was represented as a series of lines, each of whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stockholm Format
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam anDfam to disseminate protein, RNA and DNA sequence alignments. The alignment editorRaleehtml" ;"title=",;()[">,;()[aBb.-_--supports pseudoknot and further structure markup (see WUSS documentation) For protein [HGIEBTSCX] SA Surface Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) LI LIgand binding AS Active Site pAS AS - Pfam predicted sAS AS - from SwissProt IN INtron (in or after) -2 For RNA tertiary interactions: ------------------------------ tWW WC/WC in trans For basepairs: />AaBb...Zz.html" ;"title=">AaBb...Zz">>AaBb...Zz For unpaired: cWH W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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