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"Alignment-wise we weren't lined up correctly, and then a communication problem on the snap.
Alignment-wise tests for non-homogeneity were performed using two types of statistics: The number of 5% significant pairwise tests, The median of pairwise statistics.
Multiple alignments from significant local pair wise alignments.
The similarity of cochleotopic maps between subjects was tested with a pair wise alignment index (see methods).
Out of shortlisted members, those with highest pair wise alignment score with respect to DDX3X were finally chosen.
Out of these 57 sequences, those with highest pair wise alignment score with DDX3X coding sequence were kept for further study and rest were discarded.
Predicted protein sequences were imported into the ClustalX program [19] and a pair wise alignment was made using the Gonnet 250 score matrix.
Homology value (percentage of amino acid sequence identity) was calculated by pair wise alignment.
We used all unique SNV positions for calculating distance between the isolates using pair wise alignment.
Similar to step (i), dynamic programming for pair-wise alignment is used, however, each of these pair-wise group alignment yields an order of O(n) via dynamic programming (O(n)) and sum-of-pair scoring function [ 13](O(n)).
Similarly, Oliver et al. [ 23, 24] distributed the pair-wise alignment of the first step in the progressive alignment, where all pair-wise alignments are computed, on FPGA.
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