After the initial M&R, confirmation of adequate fracture reduction whilst in the procedure room was supplemented with the ultrasound by looking for alignment of the bony cortex in the two planes described (Fig. 3a,b).
First, we looked for alignment of the initial Methionine (Met) amino acid to a downstream Met in multiple proteins, which may point to the less common initial Met being an incorrect translation start position.
In one study [ 5], researchers clustered ESTs and then aligned these clusters to the genome, looking for alignments that crossed gene boundaries.
We looked for alignments between the larger potentially multimodular proteins in E. coli and smaller orthologous proteins that are homologous to only one of the modules.
Some of incorrectly oriented sequences can be detected by looking for alignments in the original direction having multiple non-consensus splices, that become all-consensus, high-identity alignments when reversed and complemented.
With the weak version of our anchored-alignment approach, we are looking for an alignment Ali wich maximum score such that the union Ali ∪ Anc is consistent.
For local alignment of primary sequences (Altschul et al., 1990; Pearson and Lipman, 1988; Smith and Waterman, 1981), one is merely looking for an alignment of contiguous linear subsequences of a query and a target.
Contending qualifications are often made needlessly exclusive, as N.B.A. fans and the media have been trained to look for a particular alignment of superstars or attempt to fit potential contenders into a specific mold.
The diagnostic criteria of MODS can be improved; we can look for a better alignment between diagnosis of MODS and its pathophysiology (uncontrolled systemic inflammation) and/or a better predictive value (mortality, post-PICU sequelae, quality of life).
Within the top five hits of the blast report, we look for the best alignment with a sequence having assigned GO terms and a sequence with assigned KO accessions, if these two sequences are not the same, then both annotations are reported in order to assign a functional annotation from both controlled vocabularies.
