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TopHat (bioinformatics)
TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites ''de novo''. TopHat aligns RNA-Seq reads to mammalian-sized genomes. History TopHat was originally developed in 2009 by Cole Trapnell, Lior Pachter and Steven Salzberg at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park and at the Mathematics Department, UC Berkeley. TopHat2 was a collaborative effort of Daehwan Kim and Steven Salzberg, initially at the University of Maryland, College Park and later at the Center for Computational Biology at Johns Hopkins University. Kim re-wrote some of Trapnell's original TopHat code in C++ to make it much faster, and added many heuristics to improve its accuracy, in a collaboration with Cole Trapnell and others. Kim and Salzberg also developed T ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms ( SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable propertie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Johns Hopkins University
Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hemisphere. It consistently ranks among the most prestigious universities in the United States and the world. The university was named for its first benefactor, the American entrepreneur and Quaker philanthropist Johns Hopkins. Hopkins' $7 million bequest to establish the university was the largest philanthropic gift in U.S. history up to that time. Daniel Coit Gilman, who was inaugurated as Johns Hopkins's first president on February 22, 1876, led the university to revolutionize higher education in the U.S. by integrating teaching and research. In 1900, Johns Hopkins became a founding member of the American Association of Universities. The university has led all U.S. universities in annual research expenditures over the past three decades. Johns Hopkins is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: * List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software **List of alignment visualization software **Alignment-free sequence analysis **De novo sequence assemblers **List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools ** List of phylogenetics software ** List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software **List of molecular graphics systems **List of protein-ligand docking software ** List of RNA structure prediction software ** List of software for protein model error verification **List of protein secondary structure prediction programs **List of protein st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Algorithms
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for ''in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Next-generation Sequencing
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1994 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run. Many NGS platforms differ in engineering configurations and sequencing chemistry. They share the technical paradigm of massive parallel sequencing via spatially separated, clonally amplified DNA templates or single DNA molecules in a flow cell. This design is very different from that of Sanger sequencing—also known as capillary sequencing or first-generation sequencing—which is based on electrophoretic separation of chain-termination products produced in individ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microarray Analysis Techniques
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA (Gene chip analysis), RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome - in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult - if not impossible - to analyze without the help of computer programs. Introduction Microarray data analysis is the final step in reading and processing data produced by a microarray chip. Samples undergo various processes including purification and scanning using the microchip, which then produces a large amount of data that requires processing via computer software. It involves several distinct steps, as outlined in the image below. Changing any one of the steps will change the outcome of the analysis, so t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of RNA-Seq Bioinformatics Tools
RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. Here are listed some of the principal tools commonly employed and links to some important web resources. Design Design is a fundamental step of a particular RNA-Seq experiment. Some important questions like sequencing depth/coverage or how many biological or technical replicates must be carefully considered. Design review. *PROPER: PROspective Power Evaluation for RNAseq. *RNAtor: an Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects. *Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. *ssizeRNA Sample Size Calculation for RNA-Seq Experimental Design. Quality control, trimming, error correction and pre-processing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tuxedo (software)
Tuxedo (Transactions for Unix, Extended for Distributed Operations) is a middleware platform used to manage distributed transaction processing in distributed computing environments. Tuxedo is a transaction processing system or transaction-oriented middleware, or enterprise application server for a variety of systems and programming languages. Developed by AT&T in the 1980s, it became a software product of Oracle Corporation in 2008 when they acquired BEA Systems. Tuxedo is now part of the Oracle Fusion Middleware. History From the beginning in 1983, AT&T designed Tuxedo for high availability and to provide extremely scalable applications to support applications requiring thousands of transactions per second on commonly available distributed systems. The original development targeted the creation and administration of operations support systems for the US telephone company that required online transaction processing (OLTP) capabilities. The Tuxedo concepts derived from the L ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term ''transcriptome'' is a portmanteau of the words ''transcript'' and ''genome''; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript chang ... [...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] |
Transcriptomics Technologies
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated. The first attempts to study whole transcriptomes began in the early 1990s. Subsequent technological advances since the late 1990s have repeatedly transformed the field and made transcriptomics a widespread discipline in biological sciences. There ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Maryland, College Park
The University of Maryland, College Park (University of Maryland, UMD, or simply Maryland) is a public land-grant research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Maryland. It is also the largest university in both the state and the Washington metropolitan area, with more than 41,000 students representing all fifty states and 123 countries, and a global alumni network of over 388,000. Together, its 12 schools and colleges offer over 200 degree-granting programs, including 92 undergraduate majors, 107 master's programs, and 83 doctoral programs. UMD is a member of the Association of American Universities and competes in intercollegiate athletics as a member of the Big Ten Conference. The University of Maryland's proximity to the nation's capital has resulted in many research partnerships with the federal government; faculty receive research funding and institutional support from many agencies, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
