One method used by the BWA alignment process to establish the correct location of an ambiguously mapping read is to attempt alignment within a limited region defined by the mapping location of the other read in the mate pair [ 31].
For each combination of paired genomes, rather than attempt alignment, we used the portable implementation of tblastx [29] available in the NCBI Blast distribution (http://www.ncbi.nlm.nih.gov/blast/download.shtml).shtml
The distal femoral condyles were resected to attempt an alignment of 6° valgus in the coronal plane.
If C[i,j] is the query gap, then Barnacle attempts an alignment between C[i,j] and C[0,i-1] + C[j + 1,|C|-1] (i.e. the concatenation of the sequence before and after the query gap).
This constraint is also in accordance with our intention for long read alignments, i.e. attempting to align a read in the full length to the genome.
An attempted re-alignment of some secret wrongness in the author's life?
While many existing 1D alignment methods have attempted to align each spectrum in a data set to a single consensus spectrum, the quality of these "star alignments" can suffer if there is wide chemical diversity between spectra, as any individual spectrum chosen as a star may not include the full complement of metabolites present in the other data sets.
For queries aligning to more than one place on the genome, strategies vary among the tools, with some reporting all alignments above certain quality threshold and others attempting to rank the alignments and report a fixed number of the top-ranking alignments.
When the insertion sequences are provided, the reference hashes are prioritized such that alignment to the MEI sequences are attempted prior to alignment to the genome reference.
The distal part of the femoral condyles was resected, attempting to achieve femorotibial alignment of 5˚ of valgus in the coronal plane.
