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APCluster: an R package for affinity propagation clustering
- Bioinformatics
, 2011
"... Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, so-called exemplars. We provide an R implementation of this promising new clustering technique to account ..."
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Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This paper introduces the package and presents an application from structural biology. Availability: The R package apcluster is available via
SETTER: web server for RNA structure comparison
- Nucleic Acids Res
, 2012
"... The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple infor-mation transfer molecule. Understanding the archi-tecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is ..."
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The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple infor-mation transfer molecule. Understanding the archi-tecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n2) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algo-rithm are freely accessible at
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt006 Structural bioinformatics Advance Access publication January 12, 2013 Fast alignment and comparison of RNA structures
, 2012
"... Motivation: To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n2)], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, ..."
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Motivation: To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n2)], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic program-ming method. Results: Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach. Availability and implementation: Source code (C and perl) and bin-aries for linux are freely available at www.zbh.uni-hamburg.de/fries. Contact:
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
, 2014
"... ABSTRACT This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multi ..."
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ABSTRACT This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do: saracoffee.
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures
, 2013
"... The R3D Align web server provides online access to ‘RNA 3D Align ’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data valid-ation and output that is more extensive and eas ..."
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The R3D Align web server provides online access to ‘RNA 3D Align ’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data valid-ation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D struc-tures, including all ribosomal RNAs, as well as guidance on effective use of the server and inter-pretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled rep-resentative structure from each group. The R3D Align web server is freely accessible at
RNA sequence and structure multiple alignments
, 2014
"... This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequen ..."
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This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve align-ment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from
STAR3D: a stack-based RNA 3D structural alignment tool
, 2015
"... The various roles of versatile non-coding RNAs typ-ically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary his-tory. Recently, many powerful tools have b ..."
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The various roles of versatile non-coding RNAs typ-ically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary his-tory. Recently, many powerful tools have been de-veloped to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly ap-plying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time.
Data and text mining Advance Access publication July 6, 2011 APCluster: an R package for affinity propagation clustering
, 2011
"... Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to acc ..."
Abstract
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Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This article introduces the package and presents an application from structural biology. Availability: The R package apcluster is available via CRAN—The Comprehensive R Archive Network:
