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224
De novo fragment assembly with short mate-paired reads: Does the read length matter?
, 2009
"... Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length Ga ..."
Abstract
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Cited by 54 (1 self)
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GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We describe a new tool, EULER-USR, for assembling mate-paired short reads and use it to analyze the question of whether the read length matters. We further complement the ongoing experimental
doi:10.1155/2008/675741 Research Article A Scaffold Analysis Tool Using Mate-Pair Information in
, 2007
"... We have developed a Windows-based program, ConPath, asascaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to fi ..."
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We have developed a Windows-based program, ConPath, asascaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
, 2013
"... Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural var ..."
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Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural
Mating Constraint Languages for Assembly Sequence Planning
- in International Conference on Robotics and Automation
, 1991
"... This paper describes and analyzes the most commonly used form of constraint languages for assembly planning: mating constraint languages. These constraints are typically composed of relations asserting that a certain pair of parts must be mated before some other pair of parts may be mated. However, ..."
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Cited by 13 (1 self)
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This paper describes and analyzes the most commonly used form of constraint languages for assembly planning: mating constraint languages. These constraints are typically composed of relations asserting that a certain pair of parts must be mated before some other pair of parts may be mated. However
Sequence analysis Advance Access publication December 2, 2013 NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
, 2013
"... Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural var ..."
Abstract
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Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural
Whom You Know Matters: Venture Capital Networks and Investment Performance,
- Journal of Finance
, 2007
"... Abstract Many financial markets are characterized by strong relationships and networks, rather than arm's-length, spot-market transactions. We examine the performance consequences of this organizational choice in the context of relationships established when VCs syndicate portfolio company inv ..."
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Cited by 138 (8 self)
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graph theory, a mathematical discipline widely used in economic sociology. 2 Graph theory provides us with tools for describing networks at a "macro" level and for measuring the relative importance, or "centrality," of each actor in the network. Our centrality measures capture five
1 Sequence analysis NextClip: an analysis and read preparation tool for Nextera long mate pair libraries
"... Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural variant ..."
Abstract
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Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. LMP libraries are an invaluable resource for carrying out complex assem-blies and other downstream bioinformatics analyses such as the characterization of structural
The RCSB Protein Data Bank: redesigned web site and web services
- Nucleic Acids Res
, 2010
"... ABSTRACT The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools ..."
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Cited by 94 (5 self)
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literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here
und Computeralgebra (CDC) Algebraic methods in analyzing lightweight cryptographic symmetric primitives
"... Algebraic methods in analyzing ..."
The Repeat Pattern Toolkit (RPT): Analyzing the Structure and Evolution of the C. elegans Genome
, 1994
"... Over 3:6 million bases of DNA sequence from chromosome III of the C. elegans have been determined. The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene densi ..."
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Cited by 22 (3 self)
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density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant local alignments (utilizing both two-way and three-way alignments), dividing the set of alignments into connected components (signifying repeat families
Results 1 - 10
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224
