PILER: identification and classification of genomic repeats.
CONCLUSIONS
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.


BACKGROUND
The PILER software is freely available at http://www.drive5.com/piler.
Edgar
Robert C
RC
bob@drive5.com
Myers
Eugene W
EW
D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D015723:Gene Library; D016678:Genome; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D018895:Microsatellite Repeats; D008957:Models, Genetic; D012984:Software; D020079:Terminal Repeat Sequences