Laxity outliers were not described and the results represent a selected group of patients with median age 60 years and knees with fixed varus- or valgus-alignment more than 10° and patients with BMI > 30 were excluded.
For most of these values, TS performed best, showing the best transcriptional coverage and parameters on CDS alignments (more than 70%) and gene expression profiles.
As expected, the blastn algorithm tended to truncate the candidate sequence alignment more frequently than the global alignment algorithms.
In addition, this mode of alignment was combined with options (−k 1 – best) that instructed Bowtie to report only the best alignment if more than one valid alignment exists.
We excluded 90 pairs after alignment because their alignments contained more than 24 gapped positions, leaving 1,813 aligned pairs of orthologs.
However, only very high quality alignments were kept, such that no alignment contained more than 3 mismatches, nor more than 9 gap positions.
For the LSU gene the PR alignment was more than 1,000 positions longer than the MF alignment, with a loss of 79 informative characters (Table 2).
Parameters for the un-gapped alignment included a maximum of three mismatches permitted in the seed, suppression of alignments if more than one reportable alignment exists, and a 'try-hard' option to find valid alignments.
Phylogenetic trees were calculated from protein alignments after removal of all portions of the alignment where more than one sequence contained gaps longer than one residue.
Without using alignment thresholds, more than 99.9% of all sequences could be aligned back to the reference.
Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive.
