Finding a longest open reading frame of an alternatively spliced gene

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

This paper provides a deterministic algorithm for finding a longest open reading frame (ORF) among all alternative splicings of a given DNA sequence. Finding protein encoding regions is a fundamental problem in genomic DNA sequence analysis and long ORFs generally provide good predictions of such regions. Although the number of splice variants is exponential in the number of optionally spliced regions, we are able to in many cases obtain quadratic or even linear performance. This efficiency is achieved by limiting the size of the search space for potential ORFs: by properly pruning the search space we can reduce the number of frames considered at any one time while guaranteeing that a longest open reading frame must be among the considered frames.

Original languageEnglish
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages215-222
Number of pages8
DOIs
StatePublished - 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Conference

Conference2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Country/TerritoryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Keywords

  • alternative splicing
  • open reading frames (ORF)
  • protein coding regions
  • String algorithms

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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