To calculate the maximum WIC score of two motifs, all possible scores of all alignments are calculated, and the maximum scoring alignment is kept.
Namely, maximum time for alignment is for particles with the lowest aspect ratio (GNPmin).
Moreover, instead of basing alignment on functionally defined areas, whose location is usually defined as the center of mass or the local maximum response, the alignment is based on patterns of response as they are distributed spatially both within and across cortical areas (Haxby et al. 2001).
Instead of basing alignment on functionally defined areas, whose location is defined as the center of mass or the local maximum response, the alignment is based on patterns of response as they are distributed spatially both within and across cortical areas.
In the case of the Needleman-Wunsch's algorithm, cell c n, n holds this value; and in the case of the Smith-Waterman's algorithm, cell c i, j with the maximum alignment score is the end point.
The constrained alignment problem is that of finding a subset of constraints, that is, a subset of edges from the bipartite similarity graph, such that the subset of edges define a legal alignment and the number of conserved edges induced by the alignment is maximum.
Maximum alignment scores are identified as the primary read; if multiple scores exist, the read is marked as ambiguous and not utilized.
During the process of a broad search, node pairs with maximum alignment scores are selected and aligned.
To make the alignment more stringent, we used two criteria: (a) maximum of two mismatches were in the seed region of the reads and maximum sum of mismatch quality across alignment is less than 70 (b) disallowing all the reads that map at multiple sites in the reference genome.
Reads with a minimum of 80%% of maximum alignment score were analysed further, after which the actual nucleotides at the potential methylation sites were summarised.
