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Title: An editing environment for DNA sequence analysis and annotation

Abstract

This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most probable gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, the authors have developed an effective way to partition a database into a set of sub-databases of related sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O({radical}N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab., TN (United States)
Sponsoring Org.:
USDOE Office of Energy Research, Washington, DC (United States)
OSTI Identifier:
563243
Report Number(s):
ORNL/CP-94756; CONF-980118-
ON: DE98000574; BR: KP1103010; TRN: AHC29803%%80
DOE Contract Number:
AC05-96OR22464
Resource Type:
Technical Report
Resource Relation:
Conference: 3. Pacific symposium on biocomputing, Kapalua, HI (United States), 5 Jan 1998; Other Information: PBD: [1998]
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; 99 MATHEMATICS, COMPUTERS, INFORMATION SCIENCE, MANAGEMENT, LAW, MISCELLANEOUS; DNA SEQUENCING; INFORMATION SYSTEMS; MOLECULAR BIOLOGY; EXPERIMENTAL DATA; GENES; DNA; MOLECULAR STRUCTURE

Citation Formats

Uberbacher, E.C., Xu, Y., Shah, M.B., Olman, V., Parang, M., and Mural, R. An editing environment for DNA sequence analysis and annotation. United States: N. p., 1998. Web. doi:10.2172/563243.
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Uberbacher, E.C., Xu, Y., Shah, M.B., Olman, V., Parang, M., & Mural, R. An editing environment for DNA sequence analysis and annotation. United States. doi:10.2172/563243.
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Uberbacher, E.C., Xu, Y., Shah, M.B., Olman, V., Parang, M., and Mural, R. Thu . "An editing environment for DNA sequence analysis and annotation". United States. doi:10.2172/563243. https://www.osti.gov/servlets/purl/563243.
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@article{osti_563243,
title = {An editing environment for DNA sequence analysis and annotation},
author = {Uberbacher, E.C. and Xu, Y. and Shah, M.B. and Olman, V. and Parang, M. and Mural, R.},
abstractNote = {This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most probable gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, the authors have developed an effective way to partition a database into a set of sub-databases of related sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O({radical}N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.},
doi = {10.2172/563243},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Dec 31 00:00:00 EST 1998},
month = {Thu Dec 31 00:00:00 EST 1998}
}
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Technical Report:
View Technical Report (0.74 MB)
DOI:  10.2172/563243
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