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Bisulfite primer design software tools | Bisulfite sequencing data analysis

Bisulfite primer design software tools | Bisulfite sequencing data analysis The major obstacle of bisulfite sequencing PCR is the reduced complexity of DNA sequences in gene promoter regions and especially CpG islands. These genomic loci have elevated GC content and lowered complexity, compared with protein-coding regions. Bisulfite treatment aggravates the situation resulting in the reduction of the four-letter alphabet to the three-letter one, except for methylated cytosines which are not converted to thymines. This strikingly decreases sequence complexity, increases mispriming and dimer-forming potential, reduces GC content, and leads to the formation of large polyT motifs. As a result, primer design is very problematic and nested PCR sometimes is required to avoid non-specific amplification.
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