Publication result detail

LTRFIND: A Novel Algorithm for Human de novo LTR Retrotransposons Identification

SEDLÁŘ, K.; PROVAZNÍK, I.

Original Title

LTRFIND: A Novel Algorithm for Human de novo LTR Retrotransposons Identification

English Title

LTRFIND: A Novel Algorithm for Human de novo LTR Retrotransposons Identification

Type

Paper in proceedings (conference paper)

Original Abstract

Modern LTR retrotransposons identification is mainly based on similarity searching using databases of known retroviruses. Nowadays, when various human genomes are available, this approach is not fast enough. Unlike the other species, human LTR retrotransposons are inactive and modified so similarity searches can hardly find these strongly mutated or previously unknown retroelements. In this paper, we present a novel algorithm for de novo identification of human LTR retrotransposons. Considering features of the human genome, we designed heuristic algorithm based on identification of long terminal repeats. Employ of exact sting match seed technique brings a very efficient search with reasonable sensitivity.

English abstract

Modern LTR retrotransposons identification is mainly based on similarity searching using databases of known retroviruses. Nowadays, when various human genomes are available, this approach is not fast enough. Unlike the other species, human LTR retrotransposons are inactive and modified so similarity searches can hardly find these strongly mutated or previously unknown retroelements. In this paper, we present a novel algorithm for de novo identification of human LTR retrotransposons. Considering features of the human genome, we designed heuristic algorithm based on identification of long terminal repeats. Employ of exact sting match seed technique brings a very efficient search with reasonable sensitivity.

Keywords

retrotransposons, LTR, human genome, exact string match

Key words in English

retrotransposons, LTR, human genome, exact string match

Authors

SEDLÁŘ, K.; PROVAZNÍK, I.

Released

24.04.2014

Publisher

LITERA

Location

Brno

ISBN

978-80-214-4924-4

Book

Proceedings of the 20th Conference STUDENT EEICT 2014

Pages from

242

Pages to

246

Pages count

5

BibTex

@inproceedings{BUT107299,
  author="Karel {Sedlář} and Valentýna {Provazník}",
  title="LTRFIND: A Novel Algorithm for Human de novo LTR Retrotransposons Identification",
  booktitle="Proceedings of the 20th Conference STUDENT EEICT 2014",
  year="2014",
  number="1.",
  pages="242--246",
  publisher="LITERA",
  address="Brno",
  isbn="978-80-214-4924-4"
}