Our simulation study demonstrates that sequence similarities and short read lengths do not rule out the accurate assessment of (differential) expression of TEs at the instance-level.
To entirely comprehend the effects and reasons of TE expression, however, it is necessary to assess the TE expression at the level of individual instances. Still, the high-throughput study of TEs is usually limited to the family or consensus-sequence level because of alignment problems prompted by high-sequence similarities and short read lengths. via DNA-methylation and histone modifications, are considered critical for maintaining genomic integrity and other functions.
Consequently, the regulations of TEs, e.g. Transposable elements (TEs) have been associated with many, frequently detrimental, biological roles.
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