SVM Based Prediction of Bacterial Transcription Start Sites
Gordon, James J. & Towsey, Michael W. (2005) SVM Based Prediction of Bacterial Transcription Start Sites. In Proceedings 6th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL’05), July 2005, Brisbane, Australia.
Identifying bacterial promoters is the key to understanding gene expression. Promoters lie in tightly constrained positions relative to the transcription start site (TSS). Knowing the TSS position, one can predict promoter positions to within a few base pairs, and vice versa. As a route to promoter identification, we formally address the problem of TSS prediction, drawing on the RegulonDB database of known (mapped) Escherichia coli TSS locations. The accepted method of finding promoters (and therefore TSSs) is to use position weight matrices (PWMs). We use an alternative approach based on sup-port vector machines (SVMs). In particular, we quantify performance of several SVM models versus a PWM approach, using area under the detection-error tradeoff (DET) curve as a performance metric. SVM models are shown to out-perform the PWM at TSS prediction, and to substantially reduce numbers of false positives, which are the bane of this problem.
Citation countsare sourced monthly fromand citation databases.
These databases contain citations from different subsets of available publications and different time periods and thus the citation count from each is usually different. Some works are not in either database and no count is displayed. Scopus includes citations from articles published in 1996 onwards, and Web of Science generally from 1980 onwards.
Citations counts from theindexing service can be viewed at the linked Google Scholar™ search.
Full-text downloadsdisplays the total number of times this work’s files (e.g., a PDF) have been downloaded from QUT ePrints as well as the number of downloads in the previous 365 days. The count includes downloads for all files if a work has more than one.
Repository Staff Only: item control page