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Infernal 1.0: Inference of RNA Alignments
 Bioinformatics
, 2009
"... Summary: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence and structurebased multiple sequence alignments. Availability: Source code, documentation, and ..."
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Summary: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence and structurebased multiple sequence alignments. Availability: Source code, documentation, and benchmark downloadable from
Genome analysis RNATOPSW: a web server for RNA structure searches of genomes
, 2009
"... Summary: RNATOPSW is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++ software package ..."
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Summary: RNATOPSW is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++ software package for the same purpose, in which filters to speed up search are manually selected. RNATOPSW improves upon RNATOPS by adding the function of automatic selection of a hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPSW complements existing RNA secondary structure search web servers that either use builtin structure profiles or are not able to detect pseudoknots. RNATOPSW inherits the efficiency of RNATOPS in detecting large, complex RNA structures. Availability: The web server RNATOPSW is available at the web site www.uga.edu/RNAInformatics/?f=software&p=RNATOPSw. The underlying search program RNATOPS can be downloaded at www.uga.edu/RNAInformatics/?f=software&p=RNATOPS. Contact:
RNATOPSW: A Web Server for RNA Structure Searches of Genomes
"... Summary: RNATOPSW is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS (Huang et al., 2008), a command line ..."
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Summary: RNATOPSW is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS (Huang et al., 2008), a command line C++ software package for the same purpose, in which filters to speed up search are manually selected. RNATOPSW improves upon RNATOPS by adding the function of automatic selection of an hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPSW complements existing RNA secondary structure search web servers that either use builtin structure profiles or are not able to detect pseudoknots. RNATOPSW inherits the efficiency of RNATOPS in detecting large, complex RNA structures. Availability: The web server RNATOPSW is available at website www.uga.edu/RNAInformatics/?f=software&p=RNATOPSw. The underlying search program RNATOPS can be downloaded at www.uga.edu/RNAInformatics/?f=software&p=RNATOPS. Contact:
On the Page Number of Secondary Structures with Pseudoknots
, 2011
"... Let S denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. {i, j} ∈ S if there is a hydrogen bond between the ith and jth nucleotide. The page number of S, denoted π(S), is the minimum number k such that S can be decomposed into a disjoint union of k second ..."
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Let S denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. {i, j} ∈ S if there is a hydrogen bond between the ith and jth nucleotide. The page number of S, denoted π(S), is the minimum number k such that S can be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NPcomplete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary structures, for which the topological genus is known. We describe two greedy algorithms, and show by an example that neither is optimal. We describe an algorithm running in time O(n log n) that produces a decomposition of an RNA structure S on n bases into at most ω(S)·log n disjoint secondary structures, where ω(S) denotes the maximum number of base pairs that may cross a given base pair. It follows that ω(S) ≤ π(S) ≤ ω(S) · log n, where π(S) denotes the page number of S. We give an O(n 3/2) time algorithm for finding a 2page decomposition of bisecondary structures for RNA sequences of size n, and we provide bounds on the expected page number of random structures having pseudoknots.
Analysis and detection of RNA pseudoknots has been quence alignments. Similar techniques were proposed by
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Treewidth and Hypertree Width
, 2014
"... The chapter covers methods for identifying islands of tractability for NPhard combinatorial problems by exploiting suitable properties of their graphical structure. Acyclic structures are considered, as well as nearly acyclic ones identified by means of socalled structural decomposition methods. ..."
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The chapter covers methods for identifying islands of tractability for NPhard combinatorial problems by exploiting suitable properties of their graphical structure. Acyclic structures are considered, as well as nearly acyclic ones identified by means of socalled structural decomposition methods. In particular, the chapter focuses on the tree decomposition method, which is the most powerful decomposition method for graphs, and on the hypertree decomposition method, which is its natural counterpart for hypergraphs. These problemdecomposition methods give rise to corresponding notions of width of an instance, namely, treewidth and hypertree width. It turns out that many NPhard problems can be solved efficiently over classes of instances of bounded treewidth or hypertree width: deciding whether a solution exists, computing a solution, and even computing an optimal solution (if some cost function over solutions is specified) are all polynomialtime tasks. Example applications include problems from artificial intelligence, databases, game theory, and combinatorial auctions.