• Login
    View Item 
    •   Home
    • UA Graduate and Undergraduate Research
    • UA Theses and Dissertations
    • Dissertations
    • View Item
    •   Home
    • UA Graduate and Undergraduate Research
    • UA Theses and Dissertations
    • Dissertations
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of UA Campus RepositoryCommunitiesTitleAuthorsIssue DateSubmit DateSubjectsPublisherJournalThis CollectionTitleAuthorsIssue DateSubmit DateSubjectsPublisherJournal

    My Account

    LoginRegister

    About

    AboutUA Faculty PublicationsUA DissertationsUA Master's ThesesUA Honors ThesesUA PressUA YearbooksUA CatalogsUA Libraries

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    A pattern matching system for biosequences.

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    azu_td_9208024_sip1_m.pdf
    Size:
    4.363Mb
    Format:
    PDF
    Description:
    azu_td_9208024_sip1_m.pdf
    Download
    Author
    Mehldau, Gerhard.
    Issue Date
    1991
    Keywords
    Molecular biology
    Computer science and scientific computing.
    Advisor
    Myers, Eugene W.
    
    Metadata
    Show full item record
    Publisher
    The University of Arizona.
    Rights
    Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
    Abstract
    String pattern matching is an extensively studied area of computer science. Over the past few decades, many important theoretical results have been discovered, and a large number of practical algorithms has been developed for efficiently matching various classes of patterns. A variety of general pattern matching tools and specialized programming languages have been implemented for applications in areas such as lexical analysis, text editing, or database searching. Most recently, the field of molecular biology has been added to the growing list of applications that make use of pattern matching technology. The requirements of biological pattern matching differ from traditional applications in several ways. First, the amount of data to be processed is very large, and hence highly efficient pattern matching tools are required. Second, the data to be searched is obtained from biological experiments, where error rates of up to 5% are not uncommon. In addition, patterns are often averaged from several, biologically similar sequences. Therefore, to be useful, pattern matching tools must be able to accommodate some notion of approximate matching. Third, formal language notations such as regular expressions, which are commonly used in traditional applications, are insufficient for describing many of the patterns that are of interest to biologists. Hence, any conventional notation must be significantly enhanced to accommodate such patterns. Taken together, these differences combine to render most existing pattern matching tools inadequate, and have created a need for specialized pattern matching systems. This dissertation presents a pattern matching system that specifically addresses the three issues outlined above. A notation for defining patterns is developed by extending the regular expression syntax in a consistent way. Using this notation, virtually any pattern of interest to biologists can be expressed in an intuitive and concise manner. The system further incorporates a very flexible notion of approximate pattern matching that unifies most of the previously developed concepts. Last, but not least, the system employs a novel, optimized backtracking algorithm, which enables it to efficiently search even very large databases.
    Type
    text
    Dissertation-Reproduction (electronic)
    Degree Name
    Ph.D.
    Degree Level
    doctoral
    Degree Program
    Computer Science
    Graduate College
    Degree Grantor
    University of Arizona
    Collections
    Dissertations

    entitlement

     
    The University of Arizona Libraries | 1510 E. University Blvd. | Tucson, AZ 85721-0055
    Tel 520-621-6442 | repository@u.library.arizona.edu
    DSpace software copyright © 2002-2017  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service operated by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.