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Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons
Stanford, California August 08-August 11
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2005.312005 IEEE Computational Systems Bioin ...
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Anantharaman Kalyanaraman, Srinivas Aluru, "Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 56-64, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), 2005.
 
 
BibTex
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@article{ 10.1109/CSB.2005.31,
author = {Anantharaman Kalyanaraman and Srinivas Aluru},
title = {Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons},
journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society},
volume = {0},
year = {2005},
isbn = {0-7695-2344-7},
pages = {56-64},
doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2005.31},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society
TI - Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons
SN - 0-7695-2344-7
SP56
EP64
A1 - Anantharaman Kalyanaraman,
A1 - Srinivas Aluru,
PY - 2005
KW - null
VL - 0
JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society
ER -
 
Anantharaman Kalyanaraman, Iowa State University
Srinivas Aluru, Iowa State University
LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software — (i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in running time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. Validation of both our serial and parallel implementations of the algorithm against the yeast genome indicates both superior quality and performance results when compared to existing software.
Citation:
Anantharaman Kalyanaraman, Srinivas Aluru, "Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons," csb, pp.56-64, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), 2005
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