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BLAT (bioinformatics)
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. It was designed primarily to decrease the time needed to align millions of mouse genomic reads and expressed sequence tags against the human genome sequence. The alignment tools of the time were not capable of performing these operations in a manner that would allow a regular update of the human genome assembly. Compared to pre-existing tools, BLAT was ~500 times faster with performing mRNA/ DNA alignments and ~50 times faster with protein/protein alignments. Overview BLAT is one of multiple algorithms developed for the analysis and comparison of biological sequences such as DNA, RNA and proteins, with a primary goal of inferring homology in order to discover biological function of genomic sequences. It is not guaranteed to find the mathematic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jim Kent
William James Kent (born February 10, 1960) is an American research scientist and computer programmer. He has been a contributor to genome database projects and the 2003 winner of the Benjamin Franklin Award. Early life Kent was born in Hawaii and grew up in San Francisco, California, United States. Computer animation Kent began his programming career in 1983 with Island Graphics Inc. where he wrote the Aegis Animator program for the Amiga home computer. This program combined polygon tweening in 3D with simple 2D cel-based animation. In 1985 he founded and ran a software company, Dancing Flame, which adapted the Aegis Animator to the Atari ST, and created Cyber Paint for that machine. Cyber Paint was a 2D animation program that brought together a wide variety of animation and paint functionality and the delta-compressed animation format developed for CAD-3D. The user could move freely between animation frames and paint arbitrarily, or utilize various animation tools for a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hash Table
In computing, a hash table, also known as hash map, is a data structure that implements an associative array or dictionary. It is an abstract data type that maps keys to values. A hash table uses a hash function to compute an ''index'', also called a ''hash code'', into an array of ''buckets'' or ''slots'', from which the desired value can be found. During lookup, the key is hashed and the resulting hash indicates where the corresponding value is stored. Ideally, the hash function will assign each key to a unique bucket, but most hash table designs employ an imperfect hash function, which might cause hash '' collisions'' where the hash function generates the same index for more than one key. Such collisions are typically accommodated in some way. In a well-dimensioned hash table, the average time complexity for each lookup is independent of the number of elements stored in the table. Many hash table designs also allow arbitrary insertions and deletions of key–value pa ... [...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 Sequence 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 sequen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acids
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotides
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular functi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA Splicing
RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcription (biology), transcript is transformed into a mature messenger RNA (Messenger RNA, mRNA). It works by removing all the introns (non-coding regions of RNA) and ''splicing'' back together exons (coding regions). For nuclear genes, nuclear-encoded genes, splicing occurs in the cell nucleus, nucleus either during or immediately after Transcription (biology), transcription. For those eukaryotic transcription, eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translation (biology), translated into protein. For many eukaryotic introns, splicing occurs in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). There exist self-splicing introns, that is, ribozymes that can catalyze their own excision from their parent RNA molecule. The process of transcription, spli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intron
An intron is any Nucleic acid sequence, nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron [i.e., gene] ... must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger – which I suggest we call introns (for intragenic regions) – alternating with regions which will be expressed – exons." (Gilbert 1978) The term ''intron'' refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA Transcription (genetics), transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons. Introns are found in the genes of most organisms and many viruses and they can be located in both protein-coding genes and genes that function as RNA (noncoding genes). There are four main types of introns: tRN ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Exons
An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. History The term ''exon'' derives from the expressed region and was coined by American biochemist Walter Gilbert in 1978: "The notion of the cistron… must be replaced by that of a transcription unit containing regions which will be lost from the mature messengerwhich I suggest we call introns (for intragenic regions)alternating with regions which will be expressedexons." This definition was originally made for protein-coding transcripts that are spliced before being transla ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic (computer Science)
In mathematical optimization and computer science, heuristic (from Greek εὑρίσκω "I find, discover") is a technique designed for solving a problem more quickly when classic methods are too slow for finding an approximate solution, or when classic methods fail to find any exact solution. This is achieved by trading optimality, completeness, accuracy, or precision for speed. In a way, it can be considered a shortcut. A heuristic function, also simply called a heuristic, is a function that ranks alternatives in search algorithms at each branching step based on available information to decide which branch to follow. For example, it may approximate the exact solution. Definition and motivation The objective of a heuristic is to produce a solution in a reasonable time frame that is good enough for solving the problem at hand. This solution may not be the best of all the solutions to this problem, or it may simply approximate the exact solution. But it is still valuabl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of California Santa Cruz
The University of California, Santa Cruz (UC Santa Cruz or UCSC) is a public university, public Land-grant university, land-grant research university in Santa Cruz, California. It is one of the ten campuses in the University of California system. Located on Monterey Bay, on the edge of the coastal community of Santa Cruz, the campus lies on of rolling, forested hills overlooking the Pacific Ocean. Founded in 1965, UC Santa Cruz began with the intention to showcase progressive, cross-disciplinary undergraduate education, innovative teaching methods and contemporary architecture. The residential college system consists of ten small colleges that were established as a variation of the Oxbridge collegiate university system. Among the Faculty is 1 Nobel Prize Laureate, 1 Breakthrough Prize in Life Sciences recipient, 12 members from the United States National Academy of Sciences, National Academy of Sciences, 28 members of the American Academy of Arts and Sciences, and 40 members o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
