ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun

• Author(s) / Creator(s)

  • Ye, C.
  • Wang, J.
  • Li, S.
  • Li, R.
  • Wong, G.K.S.
  • Ye, J.
  • Yang, H.
  • Han, Y.
  • Yu, J.

• We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

• Date created

  2005

• Subjects / Keywords

  • Evolution
  • Rice
  • Repeats
  • Tools
  • Retrotransposons
  • DNA
  • Japonica
  • Draft sequences
  • Plants
  • Maize genome

• Type of Item

  Article (Published)

• DOI

  https://doi.org/10.7939/R31V5BF2M

• License

  © 2005 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.