Three measures were computed: (i) alignment conservation annotation measures the number of conserved physicochemical properties for each column of the alignment applying the approach used in the AMAS method [ 27]; (ii) alignment quality annotation is a measure of the likelihood of observing mutations (if any) in a particular column of the alignment.
Based on the results from a previous in silico experiment using exactly the same alignment parameters as applied in this investigation we eliminated CpG sites with known alignment problems.
Maybe the most important preprocessing step is local alignment of the fluorescence images, if volume stacks are recorded alignment must be applied in (x, y, z).
Unfortunately, there are still situations where even the generalized global alignment cannot be applied in a meaningful way.
The sequence alignment was also applied in phylogenetic analyses using the neighbor-joining (PROTDIST and NEIGHBOR) and maximum parsimony (PROTPARS) programs of the PHYLIP package (ver. 3.6b).
Blue ocean strategy alignment applies not just to governments but to companies and nonprofit organizations as well (see "Comic Relief's Alignment of the Three Strategy Propositions" for more on how it works in the nonprofit sector).
Using either alignment method that was applied in a genome-wide manner (standard or IUPAC), the number of SNPs (or genes) available for allelic ratio analysis diminishes exponentially, as higher allelic depth is required (Additional file 2: Figure S1).
The ClustalW algorithm [31] and the Homology module of InsightII (version 2000 Accelrys San Diego CA) were applied in sequence alignment, and the best-fit alignment was obtained based on the Blosum scoring matrix [32] and previous alignments [16].
Currently, structure-based techniques, which use structural properties like shared relationships across sources to find alignments between concepts, are applied in combination with lexical techniques, as it has been demonstrated that it increases the overall performance [ 42- 44, 46, 47].
For instance, UBERON, Neuro-Behaviour Ontology and Phenotypic Quality Ontology were applied in the alignment process (see step one in Figure 1 and section pairwise alignment of ontology concepts with OWLSim).
However, this design is not required because most conventional structural alignment algorithms can actually be applied in this step.
