Since the structures for a given pair of full and sub alignments can vary in length, base-pair distance may be an imperfect comparison.
In each step of the iterative refinement process (Barton and Sternberg, 1987 ; Berger and Munson, 1991 ; Gotoh, 1993 ), an alignment is divided into two sub alignments and then the two sub alignments are realigned, according to the tree-dependent iterative strategy (Gotoh, 1996 ; Hirosawa et al., 1995 ), to obtain an alignment with a higher objective score.
For each of the indicated coupling strength cutoffs (colors), the frequency of contact in the 50S structure (y axis) was computed for sub alignments with different sequence depths (x axis).
Next the blue sub-alignments are aligned together.
These subgroups first were aligned in CLUSTAL X [ 56], and the resulting sub-alignments then were aligned with each other and adjusted through visual inspection and comparison to the kinase alignment of Liu and Kipreos (2000) [ 32].
ClustalW [ 31, 32] was then used to profile-align these sub-alignments, producing the final, full alignment.
129 additional sites were identified as well aligned specifically within the sub-alignment of SerRS, and 217 additional sites were identified as well aligned specifically within the sub-alignment ThrRS.
After pruning of ambiguously-aligned sites, two final sub-alignments were extracted to take into account the absence of sequence data for the head domain in one of the ctenophore sequences (PpiMHCIIb2): (i) a first alignment containing the outgroup sequences (non-class II myosins).
Each group was re-aligned with Probcons, and each of these sub-alignments was manually adjusted.
SWAMP+ combines parallelism and the novel extension producing multiple sub-alignments for pairwise comparisons.
We show that parallel versions of Smith Waterman can be successfully modified to produce multiple BLAST-like sub-alignments while maintaining the original precision.
