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    Lower bounds on multiple sequence alignment using exact 3-way alignment

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    Name:
    Lower bounds on multiple sequence ...
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    Genre
    Journal Article
    Date
    2007-04-30
    Author
    Colbourn, CJ
    Kumar, S
    Subject
    Algorithms
    Base Sequence
    DNA
    Molecular Sequence Data
    Reproducibility of Results
    Sensitivity and Specificity
    Sequence Alignment
    Sequence Analysis, DNA
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5623
    
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    DOI
    10.1186/1471-2105-8-140
    Abstract
    Background: Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently much effort has been invested in algorithms for alignment that are heuristic, or explore a restricted class of solutions. These give an upper bound on the alignment cost, but it is equally important to determine the quality of the solution obtained. In the absence of an optimal alignment with which to compare, lower bounds may be calculated to assess the quality of the alignment. As more effort is invested in improving upper bounds (alignment algorithms), it is therefore important to improve lower bounds as well. Although numerous cost metrics can be used to determine the quality of an alignment, many are based on sum-of-pairs (SP) measures and their generalizations. Results: Two standard and two new methods are considered for using exact 2-way and 3-way alignments to compute lower bounds on total SP alignment cost; one new method fares well with respect to accuracy, while the other reduces the computation time. The first employs exhaustive computation of exact 3-way alignments, while the second employs an efficient heuristic to compute a much smaller number of exact 3-way alignments. Calculating all 3-way alignments exactly and computing their average improves lower bounds on sum of SP cost in v-way alignments. However judicious selection of a subset of all 3-way alignments can yield a further improvement with minimal additional effort. On the other hand, a simple heuristic to select a random subset of 3-way alignments (a random packing) yields accuracy comparable to averaging all 3-way alignments with substantially less computational effort. Conclusion: Calculation of lower bounds on SP cost (and thus the quality of an alignment) can be improved by employing a mixture of 3-way and 2-way alignments. © 2007 Colbourn and Kumar; licensee BioMed Central Ltd.
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    BMC Bioinformatics
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    http://dx.doi.org/10.34944/dspace/5605
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      Evolutionary interactions between N-Linked glycosylation sites in the HIV-1 envelope

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      A cyclic nucleotide-gated channel mutation associated with canine daylight blindness provides insight into a role for the S2 segment Tri-Asp motif in channel biogenesis

      Tanaka, N; Delemotte, L; Klein, ML; Komáromy, AM; Tanaka, JC (2014-02-21)
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      Characterization of hARD2, a processed hARD1 gene duplicate, encoding a human protein N-α-acetyltransferase

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