Computational analysis of putative resistance gene analogs in raspberry

Angela M. Baldo, Suren Samuelian, Courtney A. Weber

    Research output: Book chapter/Published conference paperConference paperpeer-review

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    Abstract

    BioView represent an automated analysis and visualization platform developed over the last 6-7 years at HortResearch for the annotation of non genomic DNA. The system is deployed on Unix/Linux and implemented to utilize both a dedicated compute grid as well as transiently available company desktops. The system is primarily written in PERL and employs MySQL as a relational database management system for persisting data and job scheduling. The automated pipeline assembles sequences into tentative consensus sequences, and implements modules for performing BLAST comparisons, identifying simple sequence repeats and motifs, predicting single nucleotide polymorphisms and microRNA targets, designing micro-array oligonucleotides, compiling keyword dictionaries, and defining gene families. Visualizing relationships captured within the database is achieved via a web viewer. Administering the system, tracking and sharing mining efforts, initiating follow on sequencing and vector construction, performing virtual subtraction, and augmenting automated annotations by capturing end user knowledge is also undertaken via the web viewer. The system has been used to annotate databases of sequences from fungal, insect, and plant origins but functionality primarily targets those from plants. An overview of BioView sequence annotation system will be presented in context of the annotation of a Malus sequence database comprised of all HortResearch Malus ESTs, full cDNAs, and PCR product libraries merged with all Malus sequences extracted from Genbank during Feb, 2006.
    Original languageEnglish
    Title of host publication3rd International Rosaceae Genomics Conference
    Place of PublicationNZ
    PublisherRosaceae Genomics?
    Pages45
    Number of pages1
    Publication statusPublished - 2006
    EventInternational Rosaceae Genomics Conference - Napier, New Zealand, New Zealand
    Duration: 19 Mar 200622 Mar 2006

    Conference

    ConferenceInternational Rosaceae Genomics Conference
    Country/TerritoryNew Zealand
    Period19/03/0622/03/06

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