automated paleontology of repetitive dna with reannotate自动化的古生物学与reannotate重复dna.pdfVIP

BMC Genomics BioMed Central Software Open Access Automated paleontology of repetitive DNA with REANNOTATE Vini Pereira 1,2 Address: 1Department of Life Sciences, Imperial College London, Silwood Park campus, Ascot, Berkshire SL5 7PY, UK and 2Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK Email: Vini Pereira - vini.pereira@bbsrc.ac.uk Published: 18 December 2008 Received: 5 March 2008 Accepted: 18 December 2008 BMC Genomics 2008, 9:614 doi:10.1186/1471-2164-9-614 This article is available from: /1471-2164/9/614 © 2008 Pereira; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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