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    EST-PAC a web package for EST annotation and protein sequence prediction.

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    Author
    Strahm, Y; Powell, D; Lefèvre, C
    Date
    2006-10-12
    Source Title
    Source Code for Biology and Medicine
    Publisher
    Springer Science and Business Media LLC
    University of Melbourne Author/s
    Lefevre, Christophe
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
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    Document Type
    Journal Article
    Citations
    Strahm, Y., Powell, D. & Lefèvre, C. (2006). EST-PAC a web package for EST annotation and protein sequence prediction.. Source Code Biol Med, 1 (1), pp.2-. https://doi.org/10.1186/1751-0473-1-2.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256180
    DOI
    10.1186/1751-0473-1-2
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636334
    Abstract
    With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

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