BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences (Articolo in rivista)

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Label
  • BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences (Articolo in rivista) (literal)
Anno
  • 2012-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1109/TCBB.2012.30 (literal)
Alternative label
  • Felicioli C; Marangoni R (2012)
    BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences
    in IEEE/ACM transactions on computational biology and bioinformatics (Print); IEEE Computer Society, Loa Alamitos [CA] (Stati Uniti d'America)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Felicioli C; Marangoni R (literal)
Pagina inizio
  • 1120 (literal)
Pagina fine
  • 1127 (literal)
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  • http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6152085 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 9 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 4 (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Noname Res, I-56100 Pisa, Italy; Univ Pisa, Dept Comp Sci, I-56127 Pisa, Italy; Natl Res Council Italy IBF CNR, Inst Biophys, Pisa, Italy (literal)
Titolo
  • BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences (literal)
Abstract
  • Here, we propose BpMatch: an algorithm that, working on a suitably modified suffix-tree data structure, is able to compute, in a fast and efficient way, the coverage of a source sequence S on a target sequence T, by taking into account direct and reverse segments, eventually overlapped. Using BpMatch, the operator should define a priori, the minimum length l of a segment and the minimum number of occurrences minRep, so that only segments longer than l and having a number of occurrences greater than minRep are considered to be significant. BpMatch outputs the significant segments found and the computed segment-based distance. On the worst case, assuming the alphabet dimension d is a constant, the time required by BpMatch to calculate the coverage is O(l2n). On the average, by setting l>= 2 logd(n), the time required to calculate the coverage is only O(n). BpMatch, thanks to the minRep parameter, can also be used to perform a self-covering: to cover a sequence using segments coming from itself, by avoiding the trivial solution of having a single segment coincident with the whole sequence. The result of the self-covering approach is a spectral representation of the repeats contained in the sequence. BpMatch is freely available on: www.sourceforge.net/projects/bpmatch/. (literal)
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