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BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences
July-Aug. 2012 (vol. 9 no. 4)
pp. 1120-1127
ASCII Text
x 
 
R. Marangoni, C. Felicioli, "BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1120-1127, July-Aug., 2012.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2012.30,
author = {R. Marangoni and C. Felicioli},
title = {BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {9},
number = {4},
issn = {1545-5963},
year = {2012},
pages = {1120-1127},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.30},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences
IS - 4
SN - 1545-5963
SP1120
EP1127
EPD - 1120-1127
A1 - R. Marangoni,
A1 - C. Felicioli,
PY - 2012
KW - trees (mathematics)
KW - bioinformatics
KW - data structures
KW - genomics
KW - molecular biophysics
KW - molecular configurations
KW - self covering
KW - BpMatch
KW - genomic sequence segmental analysis algorithm
KW - suffix tree data structure
KW - source sequence coverage
KW - target sequence
KW - direct segments
KW - reverse segments
KW - segment based distance
KW - alphabet dimension
KW - Bioinformatics
KW - Genomics
KW - Algorithm design and analysis
KW - Image segmentation
KW - Complexity theory
KW - Evolution (biology)
KW - coverage index.
KW - Segmental analysis
KW - genomic sequences
KW - repeats
KW - inverted repeats
VL - 9
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
R. Marangoni, Dept. of Comput. Sci., Univ. of Pisa, Pisa, Italy
C. Felicioli, Noname Res., Pisa, Italy
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/.

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Index Terms:
trees (mathematics),bioinformatics,data structures,genomics,molecular biophysics,molecular configurations,self covering,BpMatch,genomic sequence segmental analysis algorithm,suffix tree data structure,source sequence coverage,target sequence,direct segments,reverse segments,segment based distance,alphabet dimension,Bioinformatics,Genomics,Algorithm design and analysis,Image segmentation,Complexity theory,Evolution (biology),coverage index.,Segmental analysis,genomic sequences,repeats,inverted repeats
Citation:
R. Marangoni, C. Felicioli, "BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1120-1127, July-Aug. 2012, doi:10.1109/TCBB.2012.30
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