A new repeat-masking method enables specific detection of homologous sequences

By Martin C. Frith. 2010

180 citations recorded by the source corpus.

Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, tantan, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA–DNA, protein–protein and DNA–protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

Subfields: Genetics, Molecular Biology

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In Genetics

1. Klaus Reuter
2. Hajk-Georg Drost
3. Benjamin Buchfink

In Molecular Biology

1. Klaus Reuter
2. Hajk-Georg Drost
3. Benjamin Buchfink

Citations in the corpus

• Sensitive protein alignments at tree-of-life scale using DIAMOND (2021, methodology): “It has been shown that despite using the SegMasker tool included in BLASTP 26 , many more and stronger spurious similarities will arise than are expected on random sequences, as defined by an e -value threshold parameter 27 .”