The CMAPi algorithm explores the entire space of possible alignments between contact maps and aligns two contact maps by optimizing the similarity function (4).
It uses existing aligner and assembler (with minor modifications to keep all possible alignments discovered, details in Section 3.1) to identify regions to which fragments align.
Finally, in some cases, aligners report only a subset of possible alignments as a result of the heuristics used.
When Bowtie encounters a short sequence that does not align to a single location, Bowtie can return all the possible alignments for that sequence read which is required by 'Bowstrap'.
Given two residues of a pair of proteins, the marginal alignment probability is equal to the accumulative probability of all possible alignments of this pair of proteins in which these two residues are aligned to each other.
He postponed the meeting, he said, to explore other possible alignments and schedules before making a final decision.
In the self-localization frame described in this article, the feature-based anchor point relation (APR) scan matching algorithm provides for each new laser scan several possible alignments within a set of reference scans.
Furthermore, different possible alignments in different parts of the site are tentatively regarded as an indication of shifting orientations to localised grids, following the shift in alignment of monumental architecture, as the settlement landscape expanded over time.
Instead, we restrict the search by considering few possibilities; in order to define the optimal pose of a given object, the alignment, which locally minimizes the visual-hull criterion (1), is taken as one of the three possible alignments obtained according to the following procedure.
HMMs can produce a single highest-scoring output but can also generate a family of possible alignments that can then be evaluated for biological significance.
To ensure that all possible alignments were found, the reference and query files were swapped and each pair was reanalyzed.
