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An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.

Publication ,  Journal Article
Singh, A; Keswani, U; Levine, D; Feschotte, C; Nikola Stojanovic,
Published in: Int J Bioinform Res Appl
2010

Interspersed repeats, mostly resulting from the activity and accumulation of transposable elements, occupy a significant fraction of many eukaryotic genomes. More than half of human genomic sequence consists of known repeats, however a very large part has not yet been associated with neither repetitive structures nor functional units. We have postulated that most of the seemingly unique content of mammalian genomes is also a result of transposon activity, written software to look for weak signals which would help us reconstruct the ancient elements with substantially mutated copies, and integrated it into a system for de novo identification and classification of interspersed repeats. In this manuscript we describe our approach, and report on our methods for building the consensus sequences of these transposons.

Duke Scholars

Published In

Int J Bioinform Res Appl

DOI

ISSN

1744-5485

Publication Date

2010

Volume

6

Issue

2

Start / End Page

147 / 162

Location

Switzerland

Related Subject Headings

  • Segmental Duplications, Genomic
  • Genomics
  • Genome
  • Eukaryota
  • DNA Transposable Elements
  • Consensus Sequence
  • Bioinformatics
  • Base Sequence
  • Algorithms
  • 49 Mathematical sciences
 

Citation

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Singh, A., Keswani, U., Levine, D., Feschotte, C., & Nikola Stojanovic, . (2010). An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. Int J Bioinform Res Appl, 6(2), 147–162. https://doi.org/10.1504/IJBRA.2010.032118
Singh, Abanish, Umeshkumar Keswani, David Levine, Cedric Feschotte, and Cedric Nikola Stojanovic. “An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.Int J Bioinform Res Appl 6, no. 2 (2010): 147–62. https://doi.org/10.1504/IJBRA.2010.032118.
Singh A, Keswani U, Levine D, Feschotte C, Nikola Stojanovic. An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. Int J Bioinform Res Appl. 2010;6(2):147–62.
Singh, Abanish, et al. “An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.Int J Bioinform Res Appl, vol. 6, no. 2, 2010, pp. 147–62. Pubmed, doi:10.1504/IJBRA.2010.032118.
Singh A, Keswani U, Levine D, Feschotte C, Nikola Stojanovic. An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. Int J Bioinform Res Appl. 2010;6(2):147–162.
Journal cover image

Published In

Int J Bioinform Res Appl

DOI

ISSN

1744-5485

Publication Date

2010

Volume

6

Issue

2

Start / End Page

147 / 162

Location

Switzerland

Related Subject Headings

  • Segmental Duplications, Genomic
  • Genomics
  • Genome
  • Eukaryota
  • DNA Transposable Elements
  • Consensus Sequence
  • Bioinformatics
  • Base Sequence
  • Algorithms
  • 49 Mathematical sciences