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DIMPL
DIMPL (Discovery of Intergenic Motifs PipeLine) is a bioinformatic pipeline that enables the extraction and selection of bacterial GC-rich intergenic regions (IGRs) that are enriched for structured non-coding RNAs (ncRNAs). The method of enriching bacterial IGRs for ncRNA motif discovery was first reported for a study in "Genome-wide discovery of structured noncoding RNAs in bacteria". DIMPL pipeline automates the process of total genome analysis by extracting IGRs, filtering them by length and nucleic acid composition, and collecting the data necessary to identify candidate motifs and assign their possible functions. DIMPL pipeline provides reproducible techniques for identifying genomic regions enriched for ncRNA through support vector machine (SVM) classifiers. It can be used to look for nucleic acid and protein motifs, including riboswitch-like elements, upstream open reading frames (uORFs), short open reading frames (sORFs), ribosomal protein leader sequences, selfish genetic el ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CarA NcRNA Motif
The carA non-coding RNA (ncRNA) is an RNA motif proposed as a Strong Riboswitch Candidate (SRC). CarA ncRNA has been recognized by a comparative sequence analysis in GC-rich intergenic regions (IGR) of bacteria, using a pipeline call Discovery of Intergenic Motifs PipeLine (DIMPL). CarA ncRNA was located upstream of ''carA'' gene which codes for the small subunit of carbamoyl phosphate synthase, which is an enzyme that catalyzes the first committed step in pyrimidine and arginine biosynthesis. CarA ncRNA has been found in bacteria of the class '' beta proteobacteria'', particularly in '' Polynucleobacter'' genus. Its proposed secondary structure consists of an extended imperfect hairpin that is immediately upstream of the predicted ribosome binding site (RBS) of the adjacent open reading frame (ORF) suggesting a possible cis-regulatory function where ligand binding regulates translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Icd-II NcRNA Motif
The icd-II non-coding RNA (ncRNA) is an RNA motif proposed as a Strong Riboswitch Candidate (SRC). Icd-II ncRNA has been recognized by a comparative sequence analysis in GC-rich intergenic regions (IGR) of bacteria, using a pipeline call Discovery of Intergenic Motifs PipeLine ( DIMPL). Icd-II ncRNA has been located upstream of the ''icd'' gene, which codes for an NADP+-dependent isocitrate dehydrogenase (IDH) enzyme. IDH is part of the citric acid cycle, and thus it participates in managing the carbon flux through this energy metabolism pathway. Icd-II ncRNA has been found in bacteria of the class '' beta proteobacteria'', particularly in '' Polynucleobacter'' genus. Icd-II RNA secondary structure consists of a three-stem junction, where the ribosome binding site (RBS) of the adjacent open reading frame (ORF) is predicted to be involved in the first base-paired stem. It has been proposed that icd-II ncRNA can function as a riboswitch that regulates translation Translatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Riboswitch
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules. The original definition of the term "riboswitch" specified that they directly sense small-molecule metabolite concentrations. Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches. Most known riboswitches occur in b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST (biotechnology)
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble alphabet above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the pig genome that resemble the mouse gene based on similarity of sequence. Background BLAST, which ''The New York Times'' called ''the Google of biological research'', is one of the most widely used bioinformatics programs for sequence searching. It addresses a fundamental problem in bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selfish Genetic Element
Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA and genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no positive or a net negative effect on organismal fitness. Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts. Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the gene-centred views of evolution popularized by George Williams and Richard Dawkins, two papers were published back-to-back in ''Nature'' in 1980 – by Leslie Orgel and Francis Crick a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosomal Protein Leader
A ribosomal protein leader is a mechanism used in cells to control the cellular concentration of a protein that forms a part of the ribosome, and to make sure that the concentration is neither too high nor too low. Ribosomal protein leaders are RNA sequences that are a part of the 5' UTR of mRNAs encoding a ribosomal protein. When cellular concentrations of the ribosomal protein are high, excess protein will bind to the mRNA leader. This binding event can lower gene expression via a number of mechanisms; for example, in the protein-bound state, the RNA could form an intrinsic transcription termination stem-loop. When cellular concentrations of the ribosomal protein are not high, they are occupied in the ribosome, and are not available in significant quantities to bind the mRNA leader. This leads to increased expression of the gene, which leads to the synthesis of more copies of the ribosomal protein. Many examples of ribosomal protein leaders are known in bacteria, including r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Reading Frame
In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a Prokaryote, prokaryotic DNA sequence, where only one of the #Six-frame translation, six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by Transcription (biology), transcription of the DNA and its subsequent interaction with the ribosome in Translation (biology), translation). Such an ORF may contain a start codon (usually AUG in terms of RNA) and by definition cannot extend beyond a stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription terminator, transcription termination site is located after the ORF, beyond the Translation (biology), translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In ... [...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] |
Pipeline (computing)
In computing, a pipeline, also known as a data pipeline, is a set of data processing elements connected in series, where the output of one element is the input of the next one. The elements of a pipeline are often executed in parallel or in time-sliced fashion. Some amount of buffer storage is often inserted between elements. Computer-related pipelines include: * Instruction pipelines, such as the classic RISC pipeline, which are used in central processing units (CPUs) and other microprocessors to allow overlapping execution of multiple instructions with the same circuitry. The circuitry is usually divided up into stages and each stage processes a specific part of one instruction at a time, passing the partial results to the next stage. Examples of stages are instruction decode, arithmetic/logic and register fetch. They are related to the technologies of superscalar execution, operand forwarding, speculative execution and out-of-order execution. * Graphics pipelines, found ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Support-vector Machine
In machine learning, support vector machines (SVMs, also support vector networks) are supervised learning models with associated learning algorithms that analyze data for classification and regression analysis. Developed at AT&T Bell Laboratories by Vladimir Vapnik with colleagues (Boser et al., 1992, Guyon et al., 1993, Cortes and Vapnik, 1995, Vapnik et al., 1997) SVMs are one of the most robust prediction methods, being based on statistical learning frameworks or VC theory proposed by Vapnik (1982, 1995) and Chervonenkis (1974). Given a set of training examples, each marked as belonging to one of two categories, an SVM training algorithm builds a model that assigns new examples to one category or the other, making it a non-probabilistic binary linear classifier (although methods such as Platt scaling exist to use SVM in a probabilistic classification setting). SVM maps training examples to points in space so as to maximise the width of the gap between the two categorie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA. Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and make up the genetic material. Nucleic acids are found in abundance in all living things, where they create, encode, and then store information of every living cell of every life-form on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded informatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
