5.Identification and masking of repeat elements

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Repeat identification Usually the first step for the genome annotation is the repeat identification and masking. With the term of "repeat" we mean different type of sequences like: Low complexity sequences as homopolymeric runs of nucleotides, transposable elements, viruses, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs).

The masking of a genome consists of two steps: 1) The built of the repeats data base and 2) the masking by using the data base.

For the construction of the repeat database we are using the RepeatModeler. RepeatModeler is a de-novo repeat family identification and modeling package.

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