AID-dependent double-strand breaks believed to be generated by deamination of nearby cytidines on both strands of sequence repeats within switch regions have been detected during CSR (Wuerffel et al., 1997; Petersen et al., 2001; Rush et al., 2004; Schrader et al., 2005).
In this setting the software will search for peaks buried within the baseline and indicate their presence with a short green bar if they are of the same wavelength and are in the same spatial position in both strands of sequence data.
Consensus RAX binding sites were searched for on both strands of promoter sequences using Possumsearch with a threshold of 80% matrix similarity [ 88].
Schmitt et al. proposed a method to label both strands of a sequence with the same barcode sequence to detect the base changes that occur in only one strand.
The entire GenBank vector sequence collection now includes information from about 3,600 entries (> 20 megabases of sequence), but this only constitutes about 5.24 × 106 unique 25 basepair sequences (both strands of the 3,600 sequences).
One of each 7-mer - reverse complement pair was then removed to avoid double-counting as both strands of upstream sequence were searched for 7-mers.
Thus, we scored both strands of each sequence region.
Both strands of each sequence were searched and possible motif locations were identified using the motif matrix score obtained from the Gibbs Motif Sampler software.
We considered both strands of each sequence (plus and minus strands) for hexamer frequency analysis, and then CPi and CNPi were calculated using Eq. 1 and Eq. 2 respectively.
To scan both strands of a sequence of length N using this approach the array must contain 2 N oligonucleotides, each with its 3'-OH immediately preceding the base to be interrogated.
