To reduce false positive targets, we set the threshold for target alignment score to 4 so that only target genes that have alignment score no greater than 4 were retained as putative targets.
Within this mix of policy, problems and politics, leaders within the bureaucracy (policy entrepreneurs) had set the stage for catalyzing stream alignment when the policy window opened with the SARS crisis.
We set the reference tree for each alignment to be the model tree that generated the data (known to us because we performed the simulation), with all zero-event branches contracted.
The alignment for this data set and subsequent maximum likelihood phylogenetic analyses was performed in MEGA4 using default parameters.
During the alignment, the "-m" setting for mismatches was set at default to allow GSNAP to auto set the number of allowed mismatches based on read length, which allowed for the best alignment across intron-exon boundaries GSNAP "soft-trims" reads during the alignment process, so that only portions of the reads above the quality threshold are aligned.
The ortholog set multiple sequence alignments for these proteins are also available in the Additional file 2 in html form.
Table 5 lists the total time it took for every program to compute the alignments for the full set of mRNA sequences.
For phylogenetic analyses, 46 outgroups and reference ITS sequences from Pezizomycetes (15), Orbilliomycetes (5), and three lichenized classes including Arthoniomycetes (15), Lichinomycetes (3), and Lecanoromycetes (8) were added to the data set for alignment and further analyses.
All proteins within each set were aligned against each other using BLAST, this resulted in 2091 alignments being returned for the training set and 2055 alignments for the test set (see Methods).
Thus, a data set with the best alignments for A r. thaliana and B ras. rapa CNSs was produced for further analysis.
