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For BWT-SW, end users usually need to post-process the results to filter out many alignments of little interest to them.
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Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways.
The metabolic pathway alignment problem definition we consider is based on the one-to-many alignments of the reaction-based pathway representations used in (Ay et al., 2011).
Within this general model, the goal is to find a global one-to-many alignment of the pathways such that a node may be mapped to a connected subgraph of many nodes.
The presence of truncated sequences in many alignments meant that the exclusion of gap sites sometimes ruled out the entire alignment (i.e., when all alignment columns had at least one gap).
The advantages of using many alignments as input to OQC becomes more apparent in our test of SV breakpoint detection in the next section.
We assessed the impact of this phenomenon on our analyzes by calculating how many alignments might end prematurely because of a contig boundary (Table 3).
For many alignment methods, rescoring of alignment-induced models using structural information can improve the separation of useful and less useful models as compared with the alignment score.
BLAST search returns many significant alignments of this tRNA with that of other arthropods, including mites (Additional file 5, 62-65).
Magnetically aligned bicelles represent one of the many alignment media used in the study of RDCs.
Many alignment algorithms exist.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com