Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: A Domain Decomposition Strategy for Alignment of Multiple Biological
  Sequences on Multiprocessor Platforms   Multiple Sequences Alignment (MSA) of biological sequences is a fundamental
problem in computational biology due to its critical significance in wide
ranging applications including haplotype reconstruction, sequence homology,
phylogenetic analysis, and prediction of evolutionary origins. The MSA problem
is considered NP-hard and known heuristics for the problem do not scale well
with increasing number of sequences. On the other hand, with the advent of new
breed of fast sequencing techniques it is now possible to generate thousands of
sequences very quickly. For rapid sequence analysis, it is therefore desirable
to develop fast MSA algorithms that scale well with the increase in the dataset
size. In this paper, we present a novel domain decomposition based technique to
solve the MSA problem on multiprocessing platforms. The domain decomposition
based technique, in addition to yielding better quality, gives enormous
advantage in terms of execution time and memory requirements. The proposed
strategy allows to decrease the time complexity of any known heuristic of
O(N)^x complexity by a factor of O(1/p)^x, where N is the number of sequences,
x depends on the underlying heuristic approach, and p is the number of
processing nodes. In particular, we propose a highly scalable algorithm,
Sample-Align-D, for aligning biological sequences using Muscle system as the
underlying heuristic. The proposed algorithm has been implemented on a cluster
of workstations using MPI library. Experimental results for different problem
sizes are analyzed in terms of quality of alignment, execution time and
speed-up.

29
The categories of this paper are: funct-an
35
The categories of this paper are: mtrl-th
36
The categories of this paper are: cmp-lg
17
The categories of this paper are: q-fin
3
The categories of this paper are: physics
13
The categories of this paper are: quant-ph
6
The categories of this paper are: astro-ph
5
The categories of this paper are: gr-qc
28
The categories of this paper are: alg-geom
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The categories of this paper are: eess
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The categories of this paper are: chao-dyn
14
The categories of this paper are: math-ph
37
The categories of this paper are: supr-con
34
The categories of this paper are: chem-ph
20
The categories of this paper are: acc-phys
15
The categories of this paper are: nucl-ex