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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 ncRN ... [...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 editorRaleehtml" ;"title=",;()[">,;()[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.html" ;"title=">AaBb...Zz">>AaBb...Zz For unpaired: cWH W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Context-free Grammar
Grammar theory to model symbol strings originated from work in computational linguistics aiming to understand the structure of natural languages. Probabilistic context free grammars (PCFGs) have been applied in probabilistic modeling of RNA structures almost 40 years after they were introduced in computational linguistics. PCFGs extend context-free grammars similar to how hidden Markov models extend regular grammars. Each 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 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 PC ... [...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 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 main areas of research ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not 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 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, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that many ... [...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 most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families. 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 biologists tracing the origins of proteins. Early genome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wikipedia
Wikipedia is a multilingual free online encyclopedia written and maintained by a community of volunteers, known as Wikipedians, through open collaboration and using a wiki-based editing system. Wikipedia is the largest and most-read reference work in history. It is consistently one of the 10 most popular websites ranked by Similarweb and formerly Alexa; Wikipedia was ranked the 5th most popular site in the world. It is hosted by the Wikimedia Foundation, an American non-profit organization funded mainly through donations. Wikipedia was launched by Jimmy Wales and Larry Sanger on January 15, 2001. Sanger coined its name as a blend of ''wiki'' and '' encyclopedia''. Wales was influenced by the " spontaneous order" ideas associated with Friedrich Hayek and the Austrian School of economics after being exposed to these ideas by the libertarian economist Mark Thornton. Initially available only in English, versions in other languages were quickly developed. Its combin ... [...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 research outputs are distributed online, 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. The main focus of the open access movement is "peer reviewed research literature". Historically, this has centered mainly on print-based academic journals. Whereas non-open access journals cover publishing costs through access tolls such as subscriptions, site licenses or pay-per-view charges, open-access journals are characterised by funding models which do not require the reader to pay to read the journal's contents, relying instead on author fees or on public funding, subsidies and sponsorships. Open access can be applied to all forms of published research output, including peer-reviewed and non peer-reviewed academic journal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Public Domain
The public domain (PD) consists of all the creative work A creative work is a manifestation of creative effort including fine artwork (sculpture, paintings, drawing, sketching, performance art), dance, writing (literature), filmmaking, and composition. Legal definitions Creative works require a cre ... to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable. Because those rights have expired, anyone can legally use or reference those works without permission. As examples, the works of William Shakespeare, Ludwig van Beethoven, 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 for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Science And Technology In Cambridgeshire
Science is a systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the universe. Science may be as old as the human species, and some of the earliest archeological evidence for scientific reasoning is tens of thousands of years old. The earliest written records in the history of science come from Ancient Egypt and Mesopotamia in around 3000 to 1200 BCE. Their contributions to mathematics, astronomy, and medicine entered and shaped Greek natural philosophy of classical antiquity, whereby formal attempts were made to provide explanations of events in the physical world based on natural causes. After the fall of the Western Roman Empire, knowledge of Greek conceptions of the world deteriorated in Western Europe during the early centuries (400 to 1000 CE) of the Middle Ages, but was preserved in the Muslim world during the Islamic Golden Age and later by the efforts of Byzantine Greek scholars who brought Greek ma ... [...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 those rights have expired, anyone can legally use or reference those works without permission. As examples, the works of William Shakespeare, Ludwig van Beethoven, 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, cooking recipes,Copyright Protection Not ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
