Sentence examples for calculate alignment from inspiring English sources

Moreover, an equation used to calculate alignment parameters of the segmented parabolic mirror is presented following the same idea.

The software's default settings were used to calculate alignment scores.

Maps of the a1 and a2 mating-type chromosomes were compared to each other with the MapSolver software (OpGen) to calculate alignment scores based on a cumulative scoring function that rewards matching cut sites and penalizes mismatch or missing sites.

Initial Model Generation In order to extract single particles from the micrographs we windowed out particles in one set of micrographs using the Boxer interface in EMAN1 (Ludtke et al., 1999 ) and used custom-built SPIDER (Frank et al., 1996 ) scripts to calculate alignment parameters between the +45° and −45° micrographs and extract the tilt mates in the other set (Leschziner, 2010 ).

In the final structure determination steps, a combination of computational tools was used: REDCAT (residual dipolar coupling analysis tool) to calculate alignment parameters (Valafar and Prestegard 2004) and XPLOR-NIH (using the GLYCAM force field; Kirschner et al. 2008) to optimize the structure via simulated annealing (Schwieters et al. 2003, 2006).

COMPASS [ 41] is a Perl script that uses Lastz [ 58] to align assembly scaffolds to a reference, after which the alignment is parsed (using SAMTools [ 75]) to calculate alignment and coverage island lengths (see Figure  7), which are used to create cumulative length plots (e.g., Figure  10), as well as to calculate coverage, validity, multiplicity, and parsimony metrics.

Specifically, to calculate alignments 'PROmer' program with the 'maxmatch' option was used.

The multi-alignment program DIALIGN [ 16, 17] has an option that can be used to calculate alignments under user-specified constraints.

Likewise, a FN is a pair in the correct alignment not present in the calculated alignment.

Also their CUDA implementation focused on calculating alignment scores only, as their main goal is optimizing database query, not the alignment itself [ 25].

k-mer searches were on average 860 times faster than blastx because the k-mer approach neither extends the matches nor calculates alignment statistics for the resulting matches.