PILER: Identification and Classification of Genomic Repeats

Bioinformatics. 2005 Jun;21 Suppl 1:i152-8. doi: 10.1093/bioinformatics/bti1003.

Abstract

Summary: Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster.

Availability: The PILER software is freely available at http://www.drive5.com/piler.

MeSH terms

  • Algorithms
  • Animals
  • Arabidopsis / genetics
  • Computational Biology / methods*
  • Drosophila melanogaster / genetics
  • Gene Library
  • Genome
  • Genome, Human
  • Genomics / methods*
  • Humans
  • Microsatellite Repeats
  • Models, Genetic
  • Software
  • Terminal Repeat Sequences