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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] |
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 properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...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] |
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] |
List Of Sequence Alignment Software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins. Database search only *Sequence type: protein or nucleotide Pairwise alignment *Sequence type: protein or nucleotide **Alignment type: local or global Multiple sequence alignment *Sequence type: protein or nucleotide. **Alignment type: local or global Genomics analysis *Sequence type: protein or nucleotide Motif finding *Sequence type: protein or nucleotide Benchmarking Alignment viewers, editors Please see List of alignment visualization software. Short-read sequence alignment See also * List of open source bioinformatics software References {{Reflist Sequence Sequence alignment software This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HMMER
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. It detects homology by comparing a ''profile-HMM'' (a Hidden Markov model constructed explicitly for a particular search) to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM. Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the ''hmmbuild'' program. The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. HMMER is a console utility ported to every major operating system, including different versions of Linux, Windows, and Mac OS. HMMER is the core utility that protein family databases such as Pfam and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xrate
XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars. It is used to discover patterns of evolutionary conservation in sequence alignments. The program can be used to estimate parameters for such models from "training" alignment data, or to apply the parameterized model so as to annotate new alignments. The program allows specification of a variety of models of DNA sequence evolution which may be arbitrarily organized using formal grammars. As an example of how XRATE is used, consider a protein-coding gene consisting of exons interspersed with introns. The exons contain triplets of nucleotides (codons) that are translated by ribosomes according to the genetic code, and consequently are under selection pressure (since any mutation may affect the translated amino acid sequence). In contrast, the introns are under fewer selective constraints and tend to evolve faster. These varying pressures show up clearly in multiple align ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Filename Extension
A filename extension, file name extension or file extension is a suffix to the name of a computer file (e.g., .txt, .docx, .md). The extension indicates a characteristic of the file contents or its intended use. A filename extension is typically delimited from the rest of the filename with a full stop (period), but in some systems it is separated with spaces. Other extension formats include dashes and/or underscores on early versions of Linux and some versions of IBM AIX. Some file systems implement filename extensions as a feature of the file system itself and may limit the length and format of the extension, while others treat filename extensions as part of the filename without special distinction. Usage Filename extensions may be considered a type of metadata. They are commonly used to imply information about the way data might be stored in the file. The exact definition, giving the criteria for deciding what part of the file name is its extension, belongs to the rules of th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Well-formed Formula
In mathematical logic, propositional logic and predicate logic, a well-formed formula, abbreviated WFF or wff, often simply formula, is a finite sequence of symbols from a given alphabet that is part of a formal language. A formal language can be identified with the set of formulas in the language. A formula is a syntactic object that can be given a semantic meaning by means of an interpretation. Two key uses of formulas are in propositional logic and predicate logic. Introduction A key use of formulas is in propositional logic and predicate logic such as first-order logic. In those contexts, a formula is a string of symbols φ for which it makes sense to ask "is φ true?", once any free variables in φ have been instantiated. In formal logic, proofs can be represented by sequences of formulas with certain properties, and the final formula in the sequence is what is proven. Although the term "formula" may be used for written marks (for instance, on a piece of paper or ch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DSSP (algorithm)
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, where it is the name of the Pascal program that implements the algorithm ''Define Secondary Structure of Proteins''. Algorithm DSSP begins by identifying the intra-backbone hydrogen bonds of the protein using a purely electrostatic definition, assuming partial charges of -0.42 ''e'' and +0.20 ''e'' to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if ''E'' in the following equation is less than -0.5 kcal/mol: : E = 0.084 \left\ \cdot 332 \, \mathrm where the r_ terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
English Alphabet
The alphabet for Modern English is a Latin-script alphabet consisting of 26 letters, each having an upper- and lower-case form. The word ''alphabet'' is a compound of the first two letters of the Greek alphabet, '' alpha'' and '' beta''. The alphabet originated around the 7th century CE to write Old English from Latin script. Since then, letters have been added or removed to give the current letters: The exact shape of printed letters varies depending on the typeface (and font), and the standard printed form may differ significantly from the shape of handwritten letters (which varies between individuals), especially cursive. English Vowels and English Consonants. The English alphabet has 6 vowels and 20 consonants. Written English has a large number of digraphs (e.g., ''would'', ''beak'', ''moat''); it stands out (almost uniquely) as a European language without diacritics in native words. The only exceptions are: * a diaeresis (e.g., "coöperation") may be us ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudoknot
__NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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