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Then, as the Blast output returns the coordinates of a partial alignment between the query and target sequences, the matched sequence was expanded to achieve the length of the query sequence.
Whilst there is partial alignment between some of the CAM practitioners consulted and the limited existing clinical evidence there are also a number of women consulting CAM practitioners for specific conditions despite an absence of clinical evidence.
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We have adopted this algorithm to generate partial alignments between the query and the target sequence.
Previous work has been published where we identified fused E. coli proteins from partial alignments between proteins encoded in the E. coli genome [ 15].
For sample #8, we assume partial alignment with an angle θ between the NR's long axis and the field direction and a maximal possible shift of 13.1 nm at θ = 0.
Partial alignment occurred by a simple balance between Brownian energy 1/2 kTBT and field-induced anisotropy energy 1/2 MΔB2, as was first proposed by Langevin and Curie (1910); where M denotes the mass of the particle and Δχ describes anisotropy per unit mass.
We keep only the partial alignments whose lengths are greater than the threshold (i.e., minimum partial alignment length).
Since a partial alignment is a locally most optimal alignment, it is not likely that a seed is extended further than the end position of the partial alignment.
The minimum partial alignment length is proportionally determined to the length of the target sequence.
Second, for each partial alignment from Step 1, seed-inserting positions are determined.
Since a partial alignment is a locally optimal alignment, the extension of a seed can be converged to the partial alignment if a seed is inserted nearby and if the score of the path is high enough.
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