Jose
Principe
alignment problem
ratio
projections
2022-09-02T16:17
axis-parallel rectangles
problem
local alignment problem
dimensions
maximum weight
false
2002
rectangle
extension
analysis
parallel rectangles
https://scigraph.springernature.com/explorer/license/
d dimensions
chapters
applications
approximation algorithm
simple approximation algorithm
performance ratio
molecular biology
technique
2002-01-01
time
129-138
goal
A Simple Approximation Algorithm for Nonoverlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles)
axis
subset
algorithm
two-phase technique
local alignment
biology
https://doi.org/10.1007/978-1-4613-0259-9_7
worst-case performance ratio
We consider the following problem motivated by applications to nonoverlapping local alignment problems in computational molecular biology: we are a given a set of n positively weighted axis parallel rectangles such that, for each axis, the projection of a rectangle on this axis does not enclose that of another, and our goal is to select a subset of independent rectangles from the given set of rectangles of total maximum weight, where two rectangles are independent provided for each axis, the projection of one rectangle does not overlap that of another. We use the two-phase technique of [3] to provide a simple approximation algorithm for this problem that runs in O(n log n) time with a worst-case performance ratio of 3. We also discuss extension and analysis of the algorithm in d dimensions.
set of rectangles
computational molecular biology
chapter
set
alignment
weight
Numerical and Computational Mathematics
pub.1014062514
dimensions_id
Mathematical Sciences
doi
10.1007/978-1-4613-0259-9_7
978-1-4613-0259-9
Biocomputing
978-1-4613-7965-2
Springer Nature
Department of Computer Science & Engineering, Pennsylvania State University, 16802, University Park, PA, USA
Department of Computer Science & Engineering, Pennsylvania State University, 16802, University Park, PA, USA
Springer Nature - SN SciGraph project
Department of Computer Science, Rutgers University, 08102, Camden, NJ, USA
Department of Computer Science, Rutgers University, 08102, Camden, NJ, USA
DasGupta
Bhaskar
Berman
Piotr
Pardalos
Panos M.