title: Automated paleontology of repetitive DNA with REANNOTATE.
abstract: BACKGROUND
  Dispersed repeats are a major component of eukaryotic genomes and drivers of genome evolution. Annotation of DNA sequences homologous to known repetitive elements has been mainly performed with the program REPEATMASKER. Sequences annotated by REPEATMASKER often correspond to fragments of repetitive elements resulting from the insertion of younger elements or other rearrangements. Although REPEATMASKER annotation is indispensable for studying genome biology, this annotation does not contain much information on the common origin of fossil fragments that share an insertion event, especially where clusters of nested insertions of repetitive elements have occurred.
  
  
  RESULTS
  Here I present REANNOTATE, a computational tool to process REPEATMASKER annotation for automated i) defragmentation of dispersed repetitive elements, ii) resolution of the temporal order of insertions in clusters of nested elements, and iii) estimating the age of the elements, if they have long terminal repeats. I have re-annotated the repetitive content of human chromosomes, providing evidence for a recent expansion of satellite repeats on the Y chromosome and, from the retroviral age distribution, for a higher rate of evolution on the Y relative to autosomes.
  
  
  CONCLUSIONS
  REANNOTATE is ready to process existing annotation for automated evolutionary analysis of all types of complex repeats in any genome. The tool is freely available under the GPL at http://www.bioinformatics.org/reannotate.
authors.affiliation: Department of Life Sciences, Imperial College London, Silwood Park campus, Ascot, Berkshire SL5 7PY, UK. vini.pereira@bbsrc.ac.uk
authors.forename: Vini
authors.initials: V
authors.lastname: Pereira
mesh_terms: D001331:Automation; D005075:Biological Evolution; D002877:Chromosomes, Human; D041322:Chromosomes, Human, Y; D004247:DNA / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D010163:Paleontology / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment
chemical_list: D004247:DNA