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A Dictionary-Based Approach for Gene Annotation

Pachter, Lior and Batzoglou, Serafim and Spitkovsky, Valentin I. and Banks, Eric and Lander, Eric S. and Kleitman, Daniel J. and Berger, Bonnie (1999) A Dictionary-Based Approach for Gene Annotation. Journal of Computational Biology, 6 (3-4). pp. 419-430. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170309-113000311

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Abstract

This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O(1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1089/106652799318364DOIArticle
http://online.liebertpub.com/doi/abs/10.1089%2F106652799318364PublisherArticle
Additional Information:© 1999 Mary Ann Liebert, Inc.
Issue or Number:3-4
Record Number:CaltechAUTHORS:20170309-113000311
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-113000311
Official Citation:Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, and Bonnie Berger. Journal of Computational Biology. July 1999, 6(3-4): 419-430. doi:10.1089/106652799318364.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74981
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:10 Mar 2017 03:57
Last Modified:03 Oct 2019 16:45

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