The alignment details of each of the 11 reads identified (listed in Table 2) reflect the predicted pattern.
Alignment details are shown in Table 1.
An important question is the choice of scores, as any particular score assignment defines the algorithm's preferences in shaping various alignment details such splicing signals or micro-exons.
Additional file 12: Alignment details.
Alignment data are stored in JSON (a lightweight data-interchange format used by JavaScript) formatted files, which contain alignment details including coordinate, sequence identity, name, e-value, etc.
It uses existing aligner and assembler (with minor modifications to keep all possible alignments discovered, details in Section 3.1) to identify regions to which fragments align.
Alignment is detailed in the Supplementary Methods.
All sequences were imported into Sequencher 5.0 (Gene Codes Corporation, Ann Arbor, MI, USA) and aligned relative to the revised Cambridge Reference Sequence for human mitochondrial DNA (rCRS [20]) using the phylogenetic alignment rules detailed in Ref. [21].
We handle this uncertainty in our P-site assignment strategy by assigning a fraction of the P-site over a neighborhood of adjacent nucleotides determined by the length and endpoints of each read alignment as detailed in the methods section of our manuscript and as previously performed in Oh et al., 2011.
To this aim, we designed randomized variants (a Null model) that preserved both the amino acids order of the wild type sequences and the column-wise frequencies of synonymous codons at each position along their alignment (see more details in Figure 1B and in the Methods section).
Among them, structural conservation was calculated based on the alignment of structural neighbors (See details in section 2.2). 25 proteins were discarded because no structures neighbors were found.
