Hardware acceleration of sequence alignment algorithms-an overview Export

@inproceedings{citeulike:3413322, abstract = {Sequence alignment is one of the most important activities in bioinformatics. With the ever increasing volume of data in bioinformatics databases, the time for comparing a query sequence with the available databases is always increasing. Many algorithms have been proposed to perform and accelerate sequence alignment activities. This paper introduces a taxonomy of the various sequence alignment algorithms found in the literature, with particular emphasis on the Smith-Waterman (S-W) algorithm. The paper also provides a classification of the available hardware acceleration methods used to speed up the S-W algorithm.}, author = {Hasan, L. and Al-Ars, Z. and Vassiliadis, S.}, booktitle = {Design \& Technology of Integrated Systems in Nanoscale Era, 2007. DTIS. International Conference on}, citeulike-article-id = {3413322}, citeulike-linkout-0 = {http://dx.doi.org/10.1109/DTIS.2007.4449499}, citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4449499}, doi = {10.1109/DTIS.2007.4449499}, journal = {Design \& Technology of Integrated Systems in Nanoscale Era, 2007. DTIS. International Conference on}, pages = {92--97}, posted-at = {2009-07-04 05:52:12}, priority = {2}, title = {Hardware acceleration of sequence alignment algorithms-an overview}, url = {http://dx.doi.org/10.1109/DTIS.2007.4449499}, year = {2007} }

TY - CONF ID - citeulike:3413322 L3 - citeulike-article-id:3413322 N2 - Sequence alignment is one of the most important activities in bioinformatics. With the ever increasing volume of data in bioinformatics databases, the time for comparing a query sequence with the available databases is always increasing. Many algorithms have been proposed to perform and accelerate sequence alignment activities. This paper introduces a taxonomy of the various sequence alignment algorithms found in the literature, with particular emphasis on the Smith-Waterman (S-W) algorithm. The paper also provides a classification of the available hardware acceleration methods used to speed up the S-W algorithm. JF - Design & Technology of Integrated Systems in Nanoscale Era, 2007. DTIS. International Conference on EP - 97 TI - Hardware acceleration of sequence alignment algorithms-an overview T2 - Design & Technology of Integrated Systems in Nanoscale Era, 2007. DTIS. International Conference on SP - 92 AU - Hasan, L AU - Al-Ars, Z AU - Vassiliadis, S PY - 2007/// UR - http://dx.doi.org/10.1109/DTIS.2007.4449499 ER -