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All Projects → lh3 → Etrf

lh3 / Etrf

Exact Tandem Repeat Finder (not a TRF replacement)

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bioinformatics

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Etrf is a simple tool to find exact tandem repeats (i.e. without mismatches or gaps in the repeat unit) in DNA sequences. It only has two parameters: the maximum repeat unit length and the minimum total repeat length. For each unit length, etrf scans an input sequence and obtains a list of non-overlapping regions no less than twice of the unit length. For two overlapping regions identified with different unit lengths, etrf chooses the longer one, or the one found with the shorter unit length if the two regions are of equal length.

Unable to find impure tandem repeats, etrf doesn't replace more sophisticated tools such as TRF or ULTRA. Nonetheless, because etrf implements an exact algorithm, it avoids ambiguity in the definition of repeats and its behavior is predicable. Etrf is also faster. It can process a human genome in 15 minutes on a single CPU thread.

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