This option, called the exclude-fragment or, for short, the xfr option, allows the user to exclude certain pairs of sites, or pairs of segments, from being aligned to each other and, this way, to introduce expert knowledge into the alignment process as well as to explore interactively various alignment alternatives.
If a pair of segments extracted from these two candidates has identity ≥0.8% closer to the query sequence than either candidate alone, a score is computed from the alignment and a chimera is reported if the score exceeds a predetermined threshold.
To help reduce the search space somewhat, the "1/2" marks show the segment (or pair of segments) halfway around the snake from the head/tail.
Similarly the pair of segments 20 and 25 probably originate from a duplication event that specifically occurred in the Glyptapanteles lineage since only one segment is present in Cotesia species.
To identify such patterns, we divided the midline of the animal to 20 equi-length segments, and quantified the fraction of time spent in quiescence by the individual angles between pairs of segments, during the period from mid L4int to the mid young adult stage.
The findings from both algorithms are discussed below, starting with the example of a specific pair of segments: NS (non-structural) and NA (neuraminidase).
We considered the aligned pairs of segments output from CHAOS to be conserved segments.
DOI: http://dx.doi.org/10.7554/eLife.05842.001 During embryo development, animals with backbones (also called vertebrates) repeatedly lay down pairs of segments along the axis that runs from the head to the tail of the embryo.
By Theorem 4.4 there exists a family (D subset S) such that (#(D) = mu) and all pairs of distinct segments from D belong either to (T_{1}) or to (T_{2}).
Whenever a pair of overlapping segments is found, the pair of IBD segments is replaced with the merged IBD segment.
The thorax has three pairs of segmented legs, one pair each for the three segments that compose the thorax and one or two pairs of wings.
