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Rfam
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's RNA WikiProject. Uses The Rfam database can be used for a variety of functions. For each ncRNA fa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rfam Logo
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, Open access (publishing), open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm Research Campus, Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar RNA structure, secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's Wikipedia:MCB, RNA WikiProject. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rfam Alignment2
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's RNA WikiProject. Uses The Rfam database can be used for a variety of functions. For each ncRNA fa ... [...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 editorRalee,;()[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">>AaBb...Zz For unpaired: cWH WC/Hoogsteen in cis cWS WC/SugarEdge in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Context-free Grammar
In theoretical linguistics and computational linguistics, probabilistic context free grammars (PCFGs) extend context-free grammars, similar to how hidden Markov models extend regular grammars. Each Formal grammar#The syntax of grammars, production is assigned a probability. The probability of a derivation (parse) is the product of the probabilities of the productions used in that derivation. These probabilities can be viewed as parameters of the model, and for large problems it is convenient to learn these parameters via machine learning. A probabilistic grammar's validity is constrained by context of its training dataset. PCFGs originated from grammar theory, and have application in areas as diverse as natural language processing to the study the structure of RNA molecules and design of programming languages. Designing efficient PCFGs has to weigh factors of scalability and generality. Issues such as grammar ambiguity must be resolved. The grammar design affects results accuracy. Gr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wellcome Trust Sanger Institute
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit organisation, non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is located on the Wellcome Genome Campus by the village of Hinxton, outside Cambridge. It shares this location with the European Bioinformatics Institute. It was established in 1992 and named after double Nobel laureate Frederick Sanger. It was conceived as a large scale DNA sequencing centre to participate in the Human Genome Project, and went on to make the largest single contribution to the gold standard sequence of the human genome. From its inception the institute established and has maintained a policy of data sharing, and does much of its research in collaboration. Since 2000, the institute expanded its mission to understand "the role of genetics in health and disease". The institute now employs around 900 people and engages in five mai ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not Translation (genetics), translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important list of RNAs, types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, Extracellular RNA, exRNAs, scaRNAs and the long noncoding RNA, long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent Transcriptomics, transcriptomic and Bioinformatics, bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have unknown functions, if any. There is no consensus on how much of non-coding transcription is functional: some believe most ncRNAs to be non-functional "junk RNA", spurious transcriptions, while others expect that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is currently provided through InterPro website. Uses The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of protein families has been widely adopted by biologists because of its wide coverage of proteins and sensible naming conventions. It is used by experimental biologists researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organise sequences and by evolutionary biologis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wikipedia
Wikipedia is a free content, free Online content, online encyclopedia that is written and maintained by a community of volunteers, known as Wikipedians, through open collaboration and the wiki software MediaWiki. Founded by Jimmy Wales and Larry Sanger in 2001, Wikipedia has been hosted since 2003 by the Wikimedia Foundation, an American 501(c)(3) organization, nonprofit organization funded mainly by donations from readers. Wikipedia is the largest and most-read reference work in history. Initially available only in English language, English, Wikipedia exists list of Wikipedias, in over 340 languages. The English Wikipedia, with over million Article (publishing), articles, remains the largest of the editions, which together comprise more than articles and attract more than 1.5 billion unique device visits and 13 million edits per month (about 5edits per second on average) . , over 25% of Wikipedia's web traffic, traffic comes from the United States, while Jap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Access (publishing)
Open access (OA) is a set of principles and a range of practices through which nominally copyrightable publications are delivered to readers free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre open access, barriers to copying or reuse are also reduced or removed by applying an open license for copyright, which regulates post-publication uses of the work. The main focus of the open access movement has been on "peer reviewed research literature", and more specifically on academic journals. This is because: * such publications have been a subject of serials crisis, unlike newspapers, magazines and fiction writing. The main difference between these two groups is in demand elasticity: whereas an English literature curriculum can substitute '' Harry Potter and the Philosopher's Stone'' with a free-domain alternative, such as '' A Voyage to Lilliput,'' an emergency room physician treating a patient for a lif ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Public Domain
The public domain (PD) consists of all the creative work to which no Exclusive exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly Waiver, waived, or may be inapplicable. Because no one holds the exclusive rights, anyone can legally use or reference those works without permission. As examples, the works of William Shakespeare, Ludwig van Beethoven, Miguel de Cervantes, Zoroaster, Lao Zi, Confucius, Aristotle, L. Frank Baum, Leonardo da Vinci and Georges Méliès are in the public domain either by virtue of their having been created before copyright existed, or by their copyright term having expired. Some works are not covered by a country's copyright laws, and are therefore in the public domain; for example, in the United States, items excluded from copyright include the formulae of Classical mechanics, Newtonian physics and cooking recipes. Other works are actively dedicated by their authors to the public domain (see waiver) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Science And Technology In Cambridgeshire
Science is a systematic discipline that builds and organises knowledge in the form of testable hypotheses and predictions about the universe. Modern science is typically divided into twoor threemajor branches: the natural sciences, which study the physical world, and the social sciences, which study individuals and societies. While referred to as the formal sciences, the study of logic, mathematics, and theoretical computer science are typically regarded as separate because they rely on deductive reasoning instead of the scientific method as their main methodology. Meanwhile, applied sciences are disciplines that use scientific knowledge for practical purposes, such as engineering and medicine. The history of science spans the majority of the historical record, with the earliest identifiable predecessors to modern science dating to the Bronze Age in Egypt and Mesopotamia (). Their contributions to mathematics, astronomy, and medicine entered and shaped the Greek natural philo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Public-domain Software With Source Code
The public domain (PD) consists of all the creative work to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable. Because no one holds the exclusive rights, anyone can legally use or reference those works without permission. As examples, the works of William Shakespeare, Ludwig van Beethoven, Miguel de Cervantes, Zoroaster, Lao Zi, Confucius, Aristotle, L. Frank Baum, Leonardo da Vinci and Georges Méliès are in the public domain either by virtue of their having been created before copyright existed, or by their copyright term having expired. Some works are not covered by a country's copyright laws, and are therefore in the public domain; for example, in the United States, items excluded from copyright include the formulae of Newtonian physics and cooking recipes. Other works are actively dedicated by their authors to the public domain (see waiver); examples include reference implem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
