Barcodes were originally detected by observing sequence alignments and locating a pair of conserved regions flanking a variable one.
A near-optimal alignment between a pair of sequences is an alignment whose score lies within the neighborhood of the optimal score.
We consider the global alignment of a pair of protein protein interaction (PPI) networks.
From the alignment, conserved regions were detected and a pair of degenerate primers was designed, with forward degenerate primer, Cys_F (5′-CTCGCTCGHTTCGCCGTCGAYGAG-3′), and reverse degenerate primer, Cys_R (5′-GTTCTTGTGHACYTCDACCTTGAA-3′).
Following the above structural alignment, a pair of aligned SSEs should have a similar position and orientation in the superposition.
We counted the number of times the best alignments of a pair of forward and reverse Sanger reads were to the same contig but with the expected opposite orientation.
Predicted protein sequences were imported into the ClustalX program [19] and a pair wise alignment was made using the Gonnet 250 score matrix.
Each candidate is made up of a contig and a pair of alignments associated with that contig.
Therefore we computed identities for all sequence pairs from an alignment and selected those pairs possessing the desired APSI ± 10%%.
Previous studies have demonstrated that the recombination patterns are related to the synaptic initiation patterns, and the region with excess of recombination is involved in chromosome alignment and pairing at an earlier stage of meiotic prophase [32] [34].
In a probabilistic setting, the optimal affine-gap alignment roughly corresponds to a viterbi path alignment from a pair-HMM with a single pair of insert and delete states [52].
