We measured both the accuracy of the resulting alignments [positive predictive value (PPV): the fraction of aligned positions that are also found in the trusted alignment] and the coverage (sensitivity: the fraction of aligned positions in the trusted alignment that are found in the calculated local alignment).
The reliability signal can be used to identify a trusted alignment region and estimate the borders of the common local motif.
Because the original BALISCORE program has certain limitations and peculiarities, e. g. skips all alignment columns with more than 20%% gaps, we instead used a modified version of COMPALIGN [ 43] called COMPALIGNP, which also calculates the fractional sequence-identity between a trusted alignment and a test alignment.
The sequences in the trusted alignment were clustered by single linkage by pairwise identity (as defined by the original alignment) and split into a smaller training alignment subset and a testing set, so as to minimize pairwise identity between training and test data and create more challenging alignment tests.
In [ 22] we used the BALISCORE, which computes the fraction of identities between a trusted reference alignment and a test alignment, where identity is defined as the averaged sequence identity over all aligned pairs of sequences.
We show how the trust alignment can be formed by considering the interactions that agents share and describe a mathematical framework to formulate precisely how the interactions support trust evaluations for both agents.
To do this, we constructed a synthetic test of realigning simulated reads generated by sampling sequence fragments from trusted (presumed correct) alignments.
Reflecting on yourself is a part of this process, but without ongoing objective feedback from trusted people, this alignment is far less likely to occur.
For a trusted RNase P multiple alignment, we used the bacterial class A seed alignment from Rfam 8.1 (Brown, 1999; Griffiths-Jones et al., 2005), and our trusted SSU rRNA alignment was adapted from the bacterial seed alignment from the Comparative RNA Web (CRW) site, (Cannone et al., 2002).
All of this is amplified by our online filter bubbles, where fake stories from "trusted" confidants and the alignment of a catchy headline or video with our own preconceptions can help to relax any innate skepticism.
