repeatconsensus

Repeatconsensus is a concept in genomics referring to the process of deriving a single representative sequence from multiple copies of a repetitive element found in a genome. The resulting consensus sequence captures the common nucleotide pattern of a repeat family, such as retrotransposons, DNA transposons, or tandem repeats, and is used to annotate and study repeats across genomes.

To compute a repeat consensus, instances of the element are identified either from de novo repeat discovery or existing repeat libraries. These instances are aligned, often with multiple sequence alignment methods tailored for repetitive DNA, and a consensus is computed per column, typically by majority base call, with allowances for gaps and ambiguous nucleotides. Some pipelines also use probabilistic models to weigh positions by base quality or evolutionary conservation, and to account for indels and nested repeats. The resulting consensus can be refined iteratively as new instances are discovered.

The consensus sequence serves as a reference in building repeat libraries, which are used by masking tools like RepeatMasker to identify and mask occurrences in genomes. It also supports classification of repeats, estimation of insertion ages, and comparative analyses of repeat evolution across species. In some projects, a set of consensus sequences forms a curated library that enables more accurate recurrence detection.

Consensus sequences may obscure genuine diversity within a repeat family, especially for highly divergent or recently active elements. If sampling of instances is biased toward a particular subfamily, the consensus may not represent others. In addition, sequencing errors and assembly artifacts can distort alignments and consensus calls.

See also: RepeatMasker, de novo repeat discovery, tandem repeats, transposable elements.