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Title:
finding optimal threshold for correction error reads in dna assembling
Author: Chin Francis Y. L. ; Leung Henry C. M. ; Li Wei-Lin ; Yiu Siu-Ming
Conference Name: 9th Asia Pacific Bioinformatics Conference
Conference Date: JAN 13-16,
Issued Date: 2009
Conference Place: Beijing, PEOPLES R CHINA
Publisher: BMC BIOINFORMATICS
Publish Place: CURRENT SCIENCE GROUP, MIDDLESEX HOUSE, 34-42 CLEVELAND ST, LONDON W1T 4LB, ENGLAND
Indexed Type: sci,istp
ISSN: 1471-2105
Department: Chin, Francis Y. L.; Leung, Henry C. M.; Yiu, Siu-Ming Univ Hong Kong, Dept Comp Sci, Pokfulam, Hong Kong, Peoples R China. Li, Wei-Lin Chinese Acad Sci, Inst software, State Key Lab Comp Sci, Beijing 100190, Peoples R China.
English Abstract: Background: DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DNA assembly algorithms. Existing algorithms, e. g. ECINDEL and SRCorr, correct the error reads by considering the number of times each length-k substring of the reads appear in the input. They treat those length-k substrings appear at least M times as correct substring and correct the error reads based on these substrings. However, since the threshold M is chosen without any solid theoretical analysis, these algorithms cannot guarantee their performances on error correction. Results: In this paper, we propose a method to calculate the probabilities of false positive and false negative when determining whether a length-k substring is correct using threshold M. Based on this optimal threshold M that minimizes the total errors ( false positives and false negatives). Experimental results on both real data and simulated data showed that our calculation is correct and we can reduce the total error substrings by 77.6% and 65.1% when compared to ECINDEL and SRCorr respectively. Conclusion: We introduced a method to calculate the probability of false positives and false negatives of the length-k substring using different thresholds. Based on this calculation, we found the optimal threshold to minimize the total error of false positive plus false negative.
Language: 英语
Citation statistics:
Content Type: 会议论文
URI: http://ir.iscas.ac.cn/handle/311060/8192
Appears in Collections:中科院软件所图书馆_2009年期刊/会议论文

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Chin Francis Y. L.,Leung Henry C. M.,Li Wei-Lin,et al. finding optimal threshold for correction error reads in dna assembling[C]. 见:9th Asia Pacific Bioinformatics Conference. Beijing, PEOPLES R CHINA. JAN 13-16,.
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