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REPuter: the manifold applications of repeat analysis on a genomic scale.
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. TheExpand
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GenDB--an open source genome annotation system for prokaryote genomes.
The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. ToExpand
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RNAshapes: an integrated RNA analysis package based on abstract shapes
TLDR
We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. Expand
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A comprehensive comparison of comparative RNA structure prediction approaches
TLDR
We evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance using comparative approaches to structure prediction. Expand
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Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
TLDR
We introduce the class of canonical simple recursive pseudoknots and present an algorithm that requires O(n4) time and O( n2) space to predict the energetically optimal structure of an RNA sequence, possible containing such pseudok nots. Expand
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Local similarity in RNA secondary structures
TLDR
We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests that allow reasonable scoring of edit operations on RNA secondary structures. Expand
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Abstract shapes of RNA.
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is ofExpand
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Fast index based algorithms and software for matching position specific scoring matrices
TLDR
We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of PSSMs in large databases. Expand
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GeneFisher-Software Support for the Detection of Postulated Genes
TLDR
When a family of genes from closely related organisms is known, there is a certain change to extract the corresponding gene from the genome of another related organism. Expand
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Pure multiple RNA secondary structure alignments: a progressive profile approach
TLDR
We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. Expand
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