Repetitive Elements: Bioinformatic Identification, Classification and Analysis

摘要: Multicopy, or repetitive, deoxyribonucleic acid (DNA) is routinely being detected and analysed by computer-assisted comparison of genomic DNA with reference databases repeats. The most representative collection repetitive elements ‘Repbase Update’ (RU), which currently contains >15 000 unique entries from diverse eukaryotic species. majority transposable (TEs) in RU are consensus sequences based on multiple alignments individual Consensus approximations active TEs responsible for generating mutated copies the genome. current two major repeat detection annotation programs, RepeatMasker CENSOR, both use repeats genomes. also increasingly used as a master library to create custom libraries newly sequenced Finally, combination different routines can be detect not similar those already present (de novo approach). Key Concepts: Active produce families subfamilies genome, called ‘interspersed elements’ ‘repeats’. Consensus derived aligned excellent they were derived. Consensus preferred screening elements, especially divergent ones. RepeatMasker CENSOR basic programs using sequence libraries. In absence sequences, characteristic structural features approach). Keywords: transposable (TEs); simple (SSRs); repeat maps; computational biology; reference