For each HMMerThread weakly conserved domain hit, the corresponding CD alignment was obtained through the use of RPS-BLAST against the CDD [2].
Optimization of rDNA gene fragment alignments was facilitated through the use of secondary structure models for teleost long and short subunit RNAs [54], [55].
Alignment may be achieved through the use of a gradient of shared axon guidance molecules, or through a retinal-matching mechanism in which axons that monitor identical regions of visual space align.
The alignment tools reviewed above could and have been used for this purpose, but only through the manual curation of the raw alignment output rather than through the use of specialized structural variant discovery tools.
YAHA is able to explore many possible alignments without sacrificing speed through the use of a number of pre-existing and novel heuristics, as well as optimized implementations of computationally intensive procedures such as seed-match sorting, banded SW and max-path graph algorithms.
While the BFAST approach is to reduce the number of candidate alignment locations generated in the seed step through the use of large spaced seeds, our approach uses a simple indexing scheme generating many candidate alignment locations, but quickly discards most of them through a series of filters.
While cellular alignment in engineered tissues can be induced through the use of external physical stimuli, there are few simple techniques for microscale control of cell behavior that are largely cell-driven.
Through the use of sequence alignments and site-directed mutagenesis we identified a single amino acid position highly correlated with the potential to degrade p53.
A portion of these nucleic and proteic data is amenable to standard computationally expensive phylogenetic analyses, through the use of multiple alignments and the construction of individual or concatenated gene phylogenies [ 1- 4].
The top 100 compounds that presented most similarity in their overlay with HU-308 (5) were of interest, these overlay results were confirmed through the use of an independent alignment program, Forge (Cresset) (Fig. 2C).
