Author: Marie Hoffmann; Michael T. Monaghan; Knut Reinert
Title: PriSeT: Efficient De Novo Primer Discovery Document date: 2020_4_7
ID: 3b3hv53b_50
Snippet: If for a length k l the melting temperature exceeds Tm max , we can reset all length bits corresponding to lengths larger or equal to k l , because Tm grows monotonously with the length of the sequence. We count the nucleotides by comparing the last two bits with the single nucleotide codes (see Table 3 ), and then apply a right shift of two until we reach the closure bit. The CG count can then directly be used to check for the CG content, which .....
Document: If for a length k l the melting temperature exceeds Tm max , we can reset all length bits corresponding to lengths larger or equal to k l , because Tm grows monotonously with the length of the sequence. We count the nucleotides by comparing the last two bits with the single nucleotide codes (see Table 3 ), and then apply a right shift of two until we reach the closure bit. The CG count can then directly be used to check for the CG content, which is recommended to be in the range of 40-60 %. However, since the CG content is relative to the sequence length, we have to check it for all encoded lengths of a TKMerID. Patterns like mono-or dinucleotide runs are detected by comparing tailing bits of the code with the two-bit encoded patterns. For example, code to detect five consecutive cytosines:
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