For the representation of kinases, we add alignment-based features, then position-specific features, and ultimately both alignment-and position-specific features.
The alignment ultimately reported by MegaBLAST may be a higher-scoring alignment with gaps.
During this latter step, we ultimately removed three alignments that were confounded by gaps, resulting in three genes with preliminary evidence of selection before correction for multiple testing.
The features one is interested in and the way in which these features are described ultimately define the correct alignment, and in theory, given a set of sequences, each feature type may define a distinct optimal alignment.
Most studies conclude with the prediction that individual and cumulative improvement in component alignment will ultimately lead to better long-term results.
The proper exon sequence could not be recovered for the macaque, however, so the region was ultimately masked from the alignment.
File format conversion was performed using the utilities for the Sequence Alignment/Map (i.e., SAM) format (SAMtools) (Li et al. 2009), and the alignment was ultimately viewed with Tablet 1.12.02.06 (Milne et al. 2010).
This alignment would ultimately create conditions that promote the spirit of co-operation, in which participation in clinical investigations is viewed as a critical way to support this important public good.
For the purposes of redundant probe set assignments and examining alternative splicing/polyadenylation, it is better to examine the exon-intron structure of target mRNAs via their genomic alignments, since ultimately these are what biologists and data analysts will use to assess whether a given pair of probes sets interrogate an alternatively spliced or polyadenylated gene.
Ultimately, the quality of an alignment will only be as good as reference alignment, regardless of the algorithm.
