Interspersed Repeat Masking Based on Protein Similarity
Query DNA sequences are compared to a
of transposable element encoded proteins. Copies of non-coding
transposable elements like SINEs and long terminal repeats of
retroviral-like elements will not be masked and the masked
sequence is not "ready" for DNA based comparisons. However, this
approach is especially useful when no repeat library is yet
available for the query species and the primary concern is
avoiding spurious matches in BLASTX-like searches. The method is
also much faster than the DNA based approach.
are minimal but be aware of the existence of transposable
element derived genes.
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Institute for Systems Biology
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Institute (NHGRI grant # RO1 HG002939).