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    BMCBI
    2011
    191views Artificial Intelligence» more  BMCBI 2011»
    RAG: An Update to the RNA-As-Graphs Resource
    13 years 4 months ago
    RAG: An Update to the RNA-As-Graphs Resource
    Download  www.biomedcentral.com
    Background: In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structur...
    Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tam...
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    BMCBI
    2011
    202views Artificial Intelligence» more  BMCBI 2011»
    R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
    13 years 7 months ago
    R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
    Download  www.biomedcentral.com
    Background: With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these mol...
    Zasha Weinberg, Ronald R. Breaker
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    IPL
    2006
    67views more  IPL 2006»
    A remark on the subsequence problem for arc-annotated sequences with pairwise nested arcs
    14 years 12 days ago
    A remark on the subsequence problem for arc-annotated sequences with pairwise nested arcs
    Download  www.cse.chalmers.se
    The Arc-Preserving Subsequence (APS) problem appears in the comparison of RNA structures in computational biology. Given two arcannotated sequences of length n and m < n, APS a...
    Peter Damaschke
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    BMCBI
    2007
    109views more  BMCBI 2007»
    Computational RNA secondary structure design: empirical complexity and improved methods
    14 years 16 days ago
    Computational RNA secondary structure design: empirical complexity and improved methods
    Download  www.biomedcentral.com
    Background: We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various cl...
    Rosalía Aguirre-Hernández, Holger H....
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    BIOSYSTEMS
    2007
    104views more  BIOSYSTEMS 2007»
    New structural variation in evolutionary searches of RNA neutral networks
    14 years 16 days ago
    New structural variation in evolutionary searches of RNA neutral networks
    Download  www.bioc.unizh.ch
    RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structu...
    Sumedha, Olivier C. Martin, Andreas Wagner
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    CPM
    2008
    Springer
    154views Combinatorics» more  CPM 2008»
    Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
    14 years 2 months ago
    Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
    Download  www.bioinf.uni-freiburg.de
    We present an algorithm for computing the edit distance of two RNA structures with arbitrary kinds of pseudoknots. A main benefit of the algorithm is that, despite the problem is N...
    Mathias Möhl, Sebastian Will, Rolf Backofen
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    BIBE
    2005
    IEEE
    121views Bioinformatics» more  BIBE 2005»
    RNA Pseudoknot Prediction Using Term Rewriting
    14 years 6 months ago
    RNA Pseudoknot Prediction Using Term Rewriting
    Download  www.cs.missouri.edu
    RNA plays a critical role in mediating every step of cellular information transfer from genes to functional proteins. Pseudoknots are widely occurring structural motifs found in a...
    Xuezheng Fu, Hao Wang, William L. Harrison, Robert...
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    COCOON
    2007
    Springer
    133views Combinatorics» more  COCOON 2007»
    Seed-Based Exclusion Method for Non-coding RNA Gene Search
    14 years 6 months ago
    Seed-Based Exclusion Method for Non-coding RNA Gene Search
    Download  www.iro.umontreal.ca
    Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-ba...
    Jean-Eudes Duchesne, Mathieu Giraud, Nadia El-Mabr...
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    WALCOM
    2010
    IEEE
    230views Algorithms» more  WALCOM 2010»
    Comparing RNA Structures with Biologically Relevant Operations Cannot Be Done without Strong Combinatorial Restrictions
    14 years 7 months ago
    Comparing RNA Structures with Biologically Relevant Operations Cannot Be Done without Strong Combinatorial Restrictions
    Download  igm.univ-mlv.fr
    Abstract. Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence a...
    Guillaume Blin, Sylvie Hamel, Stéphane Vial...
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    RECOMB
    2002
    Springer
    103views Computational Biology» more  RECOMB 2002»
    Designing RNA structures: natural and artificial selection
    15 years 22 days ago
    Designing RNA structures: natural and artificial selection
    Download  www.cs.sunysb.edu
    Barry Cohen, Steven Skiena
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