The phrase "alignment the expected" is not correct in English and does not convey a clear meaning.
It seems to be an incomplete thought or a misphrasing that lacks proper grammatical structure.
Example: "The alignment of the results was not as expected."
Alternatives: "alignment as anticipated" or "alignment to be expected".
Depending on ocular alignment, the (expected) refractive error and iris colour, cyclopentolate will be applied once, twice or three times.
Using the results from the BWA alignment, the expected mean and standard deviation of the inner distance between pairs was set for each library, and the reads were subsequently aligned to version 4.5 of the A. mellifera genome [ 44] with TopHat [ 45] version 1.4.0.
This is achieved by extending each alignment to the expected DNA fragment length according to user input.
In order to identify successful samples, the main parameters considered were the alignment length, the expected sequence match position to the sequence returned by NCBI BLASTn and the percent identity of the two sequences.
Except for Affymetrix target sequence of rat gene C1S which produced two major alignments in the q42 cytoband of rat chromosome 4, one spanning 160981068 to 160993069 with 98.6% identities and the other spanning 160609849 to 160612122 with 75.7% identities, Affymetrix target sequences of all the other twelve genes generated one major alignment to the expected gene in the human and rat genomes.
One possible explanation for the poor performance is that Bowtie2 (Langmead and Salzberg, 2012)—which works at PAUDA's core and is designed for read mapping performs poor in its local alignment mode, when the expected local alignment size is much shorter than the original read.
In the case of pairwise sequence alignment, it is possible to find an alignment that maximizes the expected AMA value using posterior decoding.
In order to find the alignment that maximizes the expected accuracy defined in (2), we first need an accurate method for estimating the posterior node alignment probability P (u i ~ v j | G).
A local alignment requires that the expected column score be negative and some column score(s) be positive.
Taking the observed distance multiplied by the alignment length as the expected effective number of substitutions and averaging the log of the mean deviation factor across the clades and the COGs, one can estimate the expected sampling error.
A linear alignment procedure for the expected range of deviations was developed for the correction of small random deviations in flow velocity and MCC temperatures and was validated using a gas mixture of analytes with a range of retention times.
