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In contrast, our model is based in the sequences of almost all the known proteins displaying prion-like behavior and we have demonstrated that our method can perform as well as PAPA for differentiating real and false prions.
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Phylogenetic trees based in rpoD sequences were constructed using the method of Maximum Likelihood.
† CG represents the quantity of CG bases in the sequences.
Degenerate bases in the sequences were assigned a specific base and the final sequences can be found in the separate excel sheet.
N50 Length is a statistical indicator of average contig length for a given assembly, defined as the length N for which 50% of all bases in the sequences are in a sequence of length L < N) [ 4].
We estimate the initial probability of leaving the background state by the number of occurrences of the initialising L-mer divided by the number of bases in the sequences.
Primer sequences used in the PCRs were chosen based on the sequences available in PRIMERBANK [ 36].
The primers were designed based on the sequences in the GenBank database.
Primer sequences used in the PCR reaction were chosen based on the sequences available in GenBank.
In conventional Sanger sequencing, the accuracy of the call of each base in the sequence can be assessed using Phred scores, which are probability-based confidence scores (Ewing et al, 1998a; Ewing and Green, 1998b).
The number of intervening letters, or bases, in the sequence determines the size of the segment.
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