North of Dundee, a more direct alignment to Azalia was added to US 23, turning the former routing back to local control in late 1947 or early 1948; at the same time, the last gravel section of the highway was paved near Hammond Bay in northwestern Presque Isle County.
Finally, a random subset of the contigs, which represented a variety of length and read coverage, were validated by direct alignment to previously published, Sanger sequenced, full-length Eucalyptus genes that were directly cloned from cDNA (Additional File 3).
The former case is particularly problematic because RNA-seq alignersometimeses prefer direct alignments to spliced alignments, causing spuriously aligned reads to accumulate on processed pseudogenes.
The different levels of conservation between these regions lead to a direct application of the syntenic global alignment to the gene prediction problem.
A jog in the routing near Almena was removed in 1937 when Wisconsin rerouted the highway to a more direct alignment in the area.
When the first set of posted routes in New York were assigned in 1924, the Barneveld Remsen portion of legislative Route 25 was bypassed by NY 12, which was assigned to Route 25's original, direct alignment between the two villages instead.
T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence.
Furthermore, if the CA1 border is placed at right angles to the alveus, that is, in direct alignment with the apices of the pyramidal cells (e.g., Barbas and Blatt 1995), then distal CA1 is likely to include deep cells that may, in fact, belong to the proximal prosubiculum, a point highlighted by Carmichael and Price (1995).
This provides additional layers of understanding and again, suggests potential directions in which the evaluation system development can proceed, in direct alignment with what the networks themselves see as the most important activities for achieving success.
As a proof of concept, AliView comes with a preset code that adds a button for directing the alignment to FastTree (Price et al., 2010) that calculates a phylogenetic tree that is then automatically opened in FigTree (Rambaut, 2012).
