Gene prediction by pattern recognition and homology search

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This paper presents an algorithm for combining pattern recognition-based exon prediction and database homology search in gene model construction. The goal is to use homologous genes or partial genes existing in the database as reference models while constructing (multiple) gene models from exon candidates predicted by pattern recognition methods. A unified framework for gene modeling is used for genes ranging from situations with strong homology to no homology in the database. To maximally use the homology information available, the algorithm applies homology on three levels: (1) exon candidate evaluation, (2) gene-segment construction with a reference model, and (3) (complete) gene ... continued below

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19 p.

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Xu, Y. & Uberbacher, E.C. May 1, 1996.

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Description

This paper presents an algorithm for combining pattern recognition-based exon prediction and database homology search in gene model construction. The goal is to use homologous genes or partial genes existing in the database as reference models while constructing (multiple) gene models from exon candidates predicted by pattern recognition methods. A unified framework for gene modeling is used for genes ranging from situations with strong homology to no homology in the database. To maximally use the homology information available, the algorithm applies homology on three levels: (1) exon candidate evaluation, (2) gene-segment construction with a reference model, and (3) (complete) gene modeling. Preliminary testing has been done on the algorithm. Test results show that (a) perfect gene modeling can be expected when the initial exon predictions are reasonably good and a strong homology exists in the database; (b) homology (not necessarily strong) in general helps improve the accuracy of gene modeling; (c) multiple gene modeling becomes feasible when homology exists in the database for the involved genes.

Physical Description

19 p.

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OSTI as DE96009720

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  • 4. international conference on intelligent systems for molecular biology, St. Louis, MO (United States), 13-15 Jun 1996

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  • Other: DE96009720
  • Report No.: CONF-9606156--1
  • Grant Number: AC05-96OR22464
  • Office of Scientific & Technical Information Report Number: 238497
  • Archival Resource Key: ark:/67531/metadc665123

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • May 1, 1996

Added to The UNT Digital Library

  • June 29, 2015, 9:42 p.m.

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  • Jan. 22, 2016, 11:10 a.m.

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Xu, Y. & Uberbacher, E.C. Gene prediction by pattern recognition and homology search, article, May 1, 1996; Tennessee. (digital.library.unt.edu/ark:/67531/metadc665123/: accessed October 18, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.