|
Fasta Fastuosa
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "fa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
William Pearson (scientist)
William Raymond Pearson is professor of biochemistry and molecular Genetics in the School of Medicine at the University of Virginia. Pearson is best known for the development of the FASTA format. Education Pearson graduated with a BS in chemistry from the University of Illinois Urbana-Champaign. He received his PhD in 1977 from Caltech. As a graduate student, he published several papers describing computer programs for analyzing biological data. Career and research After his PhD, Pearson did a postdoctoral fellowship at Johns Hopkins University. In 1983, he joined the faculty of Biochemistry at the University of Virginia School of Medicine. Immediately after joining the faculty, he collaborated with David J. Lipman at the NIH to write the FASTP program, and later FASTA. Pearson's research interests are in computational biology. He was named an American Association for the Advancement of Science (AAAS) Fellow in 2008, and an International Society for Computational Biology (ISCB) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Virginia
The University of Virginia (UVA) is a Public university#United States, public research university in Charlottesville, Virginia, United States. It was founded in 1819 by Thomas Jefferson and contains his The Lawn, Academical Village, a World Heritage Site, UNESCO World Heritage Site. The original governing Board of Visitors included three List of presidents of the United States, U.S. presidents: Jefferson, James Madison, and James Monroe, the latter as sitting president of the United States at the time of its foundation. As its first two Rector (academia)#United States, rectors, Presidents Jefferson and Madison played key roles in the university's foundation, with Jefferson designing both the #1800s, original courses of study and the university's #Academical Village, architecture. Located within its 1,135-acre central campus, the university is composed of eight undergraduate and three professional schools: the University of Virginia School of Law, School of Law, the University ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment Software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins. Database search only *Sequence type: protein or nucleotide Pairwise alignment *Sequence type: protein or nucleotide **Alignment type: local or global Multiple sequence alignment *Sequence type: protein or nucleotide. **Alignment type: local or global Genomics analysis *Sequence type: protein or nucleotide Motif finding *Sequence type: protein or nucleotide Benchmarking Alignment viewers, editors Please see List of alignment visualization software. Short-read sequence alignment See also * List of open source bioinformatics software References {{Reflist Seq Sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Histogram
A histogram is a visual representation of the frequency distribution, distribution of quantitative data. To construct a histogram, the first step is to Data binning, "bin" (or "bucket") the range of values— divide the entire range of values into a series of intervals—and then count how many values fall into each interval. The bins are usually specified as consecutive, non-overlapping interval (mathematics), intervals of a variable. The bins (intervals) are adjacent and are typically (but not required to be) of equal size. Histograms give a rough sense of the density of the underlying distribution of the data, and often for density estimation: estimating the probability density function of the underlying variable. The total area of a histogram used for probability density is always normalized to 1. If the length of the intervals on the ''x''-axis are all 1, then a histogram is identical to a relative frequency plot. Histograms are sometimes confused with bar charts. In a his ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Standard Deviation
In statistics, the standard deviation is a measure of the amount of variation of the values of a variable about its Expected value, mean. A low standard Deviation (statistics), deviation indicates that the values tend to be close to the mean (also called the expected value) of the set, while a high standard deviation indicates that the values are spread out over a wider range. The standard deviation is commonly used in the determination of what constitutes an outlier and what does not. Standard deviation may be abbreviated SD or std dev, and is most commonly represented in mathematical texts and equations by the lowercase Greek alphabet, Greek letter Sigma, σ (sigma), for the population standard deviation, or the Latin script, Latin letter ''s'', for the sample standard deviation. The standard deviation of a random variable, Sample (statistics), sample, statistical population, data set, or probability distribution is the square root of its variance. (For a finite population, v ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Similarity Measure
In statistics and related fields, a similarity measure or similarity function or similarity metric is a real-valued function that quantifies the similarity between two objects. Although no single definition of a similarity exists, usually such measures are in some sense the inverse of distance metrics: they take on large values for similar objects and either zero or a negative value for very dissimilar objects. Though, in more broad terms, a similarity function may also satisfy metric axioms. Cosine similarity is a commonly used similarity measure for real-valued vectors, used in (among other fields) information retrieval to score the similarity of documents in the vector space model. In machine learning, common kernel functions such as the RBF kernel can be viewed as similarity functions. Use of different similarity measure formulas Different types of similarity measures exist for various types of objects, depending on the objects being compared. For each type of object there ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Substitution Matrix
In bioinformatics and evolutionary biology, a substitution matrix describes the frequency at which a character in a Nucleic acid sequence, nucleotide sequence or a Protein primary structure, protein sequence changes to other character states over evolutionary time. The information is often in the form of Logit, log odds of finding two specific character states aligned and depends on the assumed number of evolutionary changes or sequence dissimilarity between compared sequences. It is an application of a stochastic matrix. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, where they are used to calculate similarity scores between the aligned sequences. Background In the process of evolution, from one generation to the next the amino acid sequences of an organism's proteins are gradually altered through the action of DNA mutations. For example, the sequence ALEIRYLRD could mutate into the sequence ALEINYLRD in one step, and pos ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oligonucleotide
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, Recombinant DNA, research, and Forensic DNA, forensics. Commonly made in the laboratory by Oligonucleotide synthesis, solid-phase chemical synthesis, these small fragments of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as Fluorescence in situ hybridization, molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules. Oligonucleotides are characterized by the Nucleic acid sequence, sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by "Monomer, -m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
K-mer
In bioinformatics, ''k''-mers are substrings of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which ''k''-mers are composed of nucleotides (''i.e''. A, T, G, and C), ''k''-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term ''k''-mer refers to all of a sequence's subsequences of length k, such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length L will have L - k + 1 ''k''-mers and there exist n^ total possible ''k''-mers, where n is number of possible monomers (e.g. four in the case of DNA). Introduction ''k''-mers are simply length k subsequences. For example, all the possible ''k''-mers of a DNA sequence are shown below: A metho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic
A heuristic or heuristic technique (''problem solving'', '' mental shortcut'', ''rule of thumb'') is any approach to problem solving that employs a pragmatic method that is not fully optimized, perfected, or rationalized, but is nevertheless "good enough" as an approximation or attribute substitution. Where finding an optimal solution is impossible or impractical, heuristic methods can be used to speed up the process of finding a satisfactory solution. Heuristics can be mental shortcuts that ease the cognitive load of making a decision. Context Gigerenzer & Gaissmaier (2011) state that sub-sets of ''strategy'' include heuristics, regression analysis, and Bayesian inference. Heuristics are strategies based on rules to generate optimal decisions, like the anchoring effect and utility maximization problem. These strategies depend on using readily accessible, though loosely applicable, information to control problem solving in human beings, machines and abstract i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
T-Coffee
T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from Protein Data Bank (PDB) files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF, and FASTA format. The most common input formats are supported (FASTA, Protein Information Resource (PIR)). Algorithm T-Coffee algorithm consist of two main features, the first by, using heterogeneous data sources, can provide simple and flexible means to generate multiple alignments. T-coffee can compute multiple alignments using a library that was generat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
