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Optimizing Multiple Seeds for Protein Homology Search
January-March 2005 (vol. 2 no. 1)
pp. 29-38
ASCII Text
x 
 
Daniel G. Brown, "Optimizing Multiple Seeds for Protein Homology Search," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 29-38, January-March, 2005.
 
 
BibTex
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@article{ 10.1109/TCBB.2005.13,
author = {Daniel G. Brown},
title = {Optimizing Multiple Seeds for Protein Homology Search},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {2},
number = {1},
issn = {1545-5963},
year = {2005},
pages = {29-38},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2005.13},
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 - Optimizing Multiple Seeds for Protein Homology Search
IS - 1
SN - 1545-5963
SP29
EP38
EPD - 29-38
A1 - Daniel G. Brown,
PY - 2005
KW - Bioinformatics database applications
KW - similarity measures
KW - biology and genetics.
VL - 2
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
We present a framework for improving local protein alignment algorithms. Specifically, we discuss how to extend local protein aligners to use a collection of vector seeds or ungapped alignment seeds to reduce noise hits. We model picking a set of seed models as an integer programming problem and give algorithms to choose such a set of seeds. While the problem is NP-hard, and Quasi-NP-hard to approximate to within a logarithmic factor, it can be solved easily in practice. A good set of seeds we have chosen allows four to five times fewer false positive hits, while preserving essentially identical sensitivity as BLASTP.

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Index Terms:
Bioinformatics database applications, similarity measures, biology and genetics.
Citation:
Daniel G. Brown, "Optimizing Multiple Seeds for Protein Homology Search," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 29-38, Jan.-March 2005, doi:10.1109/TCBB.2005.13
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