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Absent sequences: Nullomers and primes

  • Boise State University

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

74 Scopus citations

Abstract

We describe a new publicly available algorithm for identifying absent sequences, and demonstrate its use by listing the smallest oligomers not found in the human genome (human nullomers), and those not found in any reported genome or GenBank sequence (primes). These absent sequences define the maximum set of potentially lethal oligomers. They also provide a rational basis for choosing artificial DNA sequences for molecular barcodes, show promise for species identification and environmental characterization based on absence, and identify potential targets for therapeutic intervention and suicide markers.

Original languageEnglish
Title of host publicationPacific Symposium on Biocomputing 2007, PSB 2007
PublisherWorld Scientific
Pages355-366
Number of pages12
ISBN (Print)9812704175, 9789812704177
DOIs
StatePublished - 2007
Event12th Pacific Symposium on Biocomputing, PSB 2007 - Maui, HI, United States
Duration: 3 Jan 20077 Jan 2007

Publication series

NamePacific Symposium on Biocomputing 2007, PSB 2007

Conference

Conference12th Pacific Symposium on Biocomputing, PSB 2007
Country/TerritoryUnited States
CityMaui, HI
Period3/01/077/01/07

Keywords

  • Algorithms
  • Base Sequence
  • Computational Biology
  • DNA/genetics
  • Databases, Genetic
  • Genome, Human
  • Humans
  • Sequence Analysis/statistics & numerical data
  • Sequence Analysis, DNA/statistics & numerical data
  • Software

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