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Automated Molecular Paleontology of Complex DNA RepeatsBackground: 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. Repeats may become fragmented by the insertion of younger elements or other rearrangements. RepeatMasker annotation is indispensable for studying genome biology but does not contain much information on the common origin of fossil repeat fragments that share an insertion event, especially where clusters of nested insertions have occurred.REannotate is 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, iii) estimating the age of the elements, if they have long terminal repeats (LTRs). REannotate is ready to process existing annotation for automated evolutionary analysis of all types of complex repeats in any genome. The tool (and Perl source code) is freely available underl the GNU Public License.
Vini Pereira Last modified: Fri Jan 25 21:05:56 GMT 2008 |