Results obtained with this or the previous alignment protocol are very similar, reinforcing the quality of our results.
A comprehensive explanation of DNA extraction, PCR, and alignment protocols is given in [ 81].
The protocol was adapted from Nature protocols.
This is partly because of the extreme diversity of the gene family and partly because many predicted proteins from P. falciparum contain large repetitive insertions (Hidden Markov Model-based alignment protocols would be expected to cope better in these circumstances than other common methods).
The starting point of the new detection protocol are multiple sequence alignments which can be obtained as described in the following, or assembled with alternative methods preferred by the user.
The first step in the regular analysis protocol is based on the alignment of millions of short sequences obtained from each run.
The computing resources necessary for this protocol are heavy, particularly for the alignment of sequencing reads to the reference genome.
