Publication 2005 Issue No. 1 - January-March Abstract - Optimizing Multiple Seeds for Protein Homology Search
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 x @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 - JOURJO - IEEE/ACM Transactions on Computational Biology and BioinformaticsTI - Optimizing Multiple Seeds for Protein Homology SearchIS - 1SN - 1545-5963SP29EP38EPD - 29-38A1 - Daniel G. Brown, PY - 2005KW - Bioinformatics database applicationsKW - similarity measuresKW - biology and genetics.VL - 2JA - IEEE/ACM Transactions on Computational Biology and BioinformaticsER -
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