Table 1

The four potential di-nucleotide RIP mutations detected by RIPCAL.

RIP mutation

Counted di-nucleotides

Forward

Reverse complement

Forward

Reverse complement


pre-RIP

post-RIP

pre-RIP

post-RIP


CpA

TpA

TpG

TpA

CpA, TpA

TpG, TpA

CpC

TpC

GpG

GpA

CpC, TpC

GpG, GpA

CpG

TpG

CpG

CpA

CpG, TpG

CpG, CpA

CpT

TpT

ApA

ApG

CpT, TpT

ApG, ApA


The deRIP process counts the occurrence of the contributing di-nucleotides incrementally across a multiple alignment of repeats and alters the consensus sequence at each position to the appropriate pre-RIP di-nucleotide sequence.

Hane and Oliver BMC Genomics 2010 11:655   doi:10.1186/1471-2164-11-655

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