Efficient representation of DNA data for pattern recognition using failure factor oracles

Loek Cleophas, Derrick G. Kourie, Bruce W. Watson

    Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

    Abstract

    In indexing of and pattern matching on DNA sequences, representing all factors of a sequence is important. One efficient, compact representation is the factor oracle (FO). At the same time, any classical deterministic finite automata (DFA) can be transformed to a so-called failure one (FDFA), which may use failure transitions to replace multiple symbol transitions, potentially yielding a more compact representation. We combine the two ideas and directly construct a failure factor oracle (FFO) from a given sequence, in contrast to ex post facto transformation to an FDFA. The algorithm is suitable for long sequences. We empirically compared the resulting FFOs and FOs on number of transitions for many DNA sequences of lengths 4• 512, showing gains of up to 10%in total number of transitions, with failure transitions also taking up less space than symbol transitions. Preliminary results on sequence processing runtimes when using FFOs originally showed these to be multiples of those when using FOs, but partial memoization already leads to drastic improvements. Altogether the results are promising, particularly for the use of FFOs for (repeated) factor detection, where recognition speed may be less important than memory use.

    Original languageEnglish
    Title of host publicationSAICSIT '13 : Proceedings of the South African Institute for Computer Scientists and Information Technologists Conference, 7-9 October 2013, East London, South Africa
    Place of PublicationNew York
    PublisherAssociation for Computing Machinery, Inc
    Pages369-377
    Number of pages9
    ISBN (Print)9781450321129
    DOIs
    Publication statusPublished - 2013
    Event2013 Annual Research Conference of the South African Institute of Computer Scientists and Information Technologists (SAICSIT 2013) - Blue Lagoon Hotel & Conference Centre, East London, South Africa
    Duration: 7 Oct 20139 Oct 2013
    http://www.ict.ru.ac.za/saicsit2013/

    Conference

    Conference2013 Annual Research Conference of the South African Institute of Computer Scientists and Information Technologists (SAICSIT 2013)
    Abbreviated titleSAICSIT 2013
    CountrySouth Africa
    CityEast London
    Period7/10/139/10/13
    Other“A Connected Society”
    Internet address

    Keywords

    • Algorithmics
    • Dictionary
    • DNA sequences
    • Pattern matching

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