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MochiView
MochiView (''Mo''tif and ''ChI''P ''View''er) Homann OR and Johnson AD. MochiView: versatile software for genome browsing and DNA Motif analysis. BMC Biology. 2010, 8:4/ref> is software that integrates a genome browser and tools for data and Sequence motif visualization and analysis. The software uses the Java language, contains a fully integrated JavaDB database, is platform-independent, and is freely available. Description MochiView was originally designed as a platform for rapidly browsing, visualizing, and extracting Sequence motifs from ChIP-chip and ChIP-Seq data. The software uses a generalized data format that serves other purposes as well, such as the visualization and analysis of RNA-Seq data or the import, maintenance, exploration, and analysis of Sequence motif libraries. The MochiView website [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Browser
The completion of the human genome sequencing in the early 2000s was a turning point in genomics research. Scientists have conducted series of research into the activities of genes and the genome as a whole. The human genome contains around 3 billion base pairs nucleotide, and the huge quantity of data created necessitates the development of an accessible tool to explore and interpret this information in order to investigate the genetic basis of disease, evolution, and biological processes. The field of genomics has continued to grow, with new sequencing technologies and computational tool making it easier to study the genome. The genome browser is an important tool for studying the genome. In bioinformatics, a genome browser is a graphical interface for displaying information from a biological database for genomic data. It is a software tool that displays genetic data in graphical form. Genome browsers enable users to visualize and browse entire genomes with annotated data, includi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Language
Java is a high-level, general-purpose, memory-safe, object-oriented programming language. It is intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. Java gained popularity shortly after its release, and has been a popular programming language since then. Java was the third most popular programming language in according to GitHub. Although still widely popular, there has been a gradual decline in use of Java in recent years with other langu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaDB
Apache Derby (previously distributed as IBM Cloudscape) is a relational database management system (RDBMS) developed by the Apache Software Foundation that can be embedded in Java programs and used for online transaction processing. It has a 3.5 MB disk-space footprint. Apache Derby is developed as an open source project under the Apache 2.0 license. For a time, Oracle distributed the same binaries under the name Java DB. In June 2015 they announced that for JDK 9 they would no longer be doing so. History Apache Derby originated at Cloudscape Inc, an Oakland, California, start-up founded in 1996 by Nat Wyatt and Howard Torf to develop Java database technology. The first release of the database engine, then called JBMS, was in 1997. Subsequently, the product was renamed Cloudscape and releases were made about every six months. In 1999, Informix Software, Inc., acquired Cloudscape, Inc. In 2001 IBM acquired the database assets of Informix Software, including Cloudscape. The data ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP-chip
ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray (''"chip"''). Like regular Ch-IP, ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA ''in vivo''. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, DNA replication, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications. The goal of ChIP-on-chip is to locate protein binding sites that may help identify functional elements in the genome. For example, in the case of a tran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP-Seq
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with Massively parallel signature sequencing, massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations. Uses ChIP-seq is primarily used to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. This epigenetic information is complementary to genotype and expression analysis. ChIP-seq technology is currently seen primarily as an alternative to ChIP-chip which requires a protein microarray, hybridization ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA-Seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome. RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/ SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments. In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, bulk RNA sequencing, 3' mRNA-sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of California At San Francisco
The University of California, San Francisco (UCSF) is a public land-grant research university in San Francisco, California, United States. It is part of the University of California system and is dedicated entirely to health science and life science. It conducts research and teaching in medical and biological sciences. UCSF was founded as Toland Medical College in 1864. In 1873, it became affiliated with the University of California as its Medical Department. In the same year, it incorporated the California College of Pharmacy and in 1881 it established a dentistry school. Its facilities were located in both Berkeley and San Francisco. In 1964, the school gained full administrative independence as a campus of the UC system, headed by its own chancellor, and in 1970 it gained its current name. Historically based at Parnassus Heights with satellite facilities throughout the city, UCSF developed a second major campus in the newly redeveloped Mission Bay district in the early 20 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
