Abstract

An algorithm has been developed for the determination of nucleotide sequence from data produced in fluorescence-based automated DNA sequencing instruments employing the four-color strategy. This algorithm takes advantage of object oriented programming techniques for modularity and extensibility. The algorithm is adaptive in that data sets from a wide variety of instruments and sequencing conditions can be used with good results. Confidence values are provided on the base calls as an estimate of accuracy. The algorithm iteratively employs confidence determinations from several different modules, each of which examines a different feature of the data for accurate peak identification. Modules within this system can be added or removed for increased performance or for application to a different task. In comparisons with commercial software, the algorithm performed well.

Keywords

SoftwareBiologyModularity (biology)ExtensibilityObject (grammar)DNA sequencingTask (project management)Object-oriented programmingSequence (biology)Computer scienceData miningAlgorithmArtificial intelligenceDNAProgramming languageGeneticsEngineering

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Publication Info

Year
1993
Type
article
Volume
21
Issue
19
Pages
4530-4540
Citations
51
Access
Closed

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Michael C. Giddings, Robert L. Brumley, Michael Haker et al. (1993). An adaptive, object oriented strategy for base calling in DNA sequence analysis. Nucleic Acids Research , 21 (19) , 4530-4540. https://doi.org/10.1093/nar/21.19.4530

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DOI
10.1093/nar/21.19.4530