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In order to increase speed, alignment was executed in parallel using the westgrid resource.
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Two sinusoidal curves appear after the light path alignment is executed.
Multiple sequence alignments were executed using Clustal W (http://www.clustal.org) with default parameters.
Domain-based alignments were executed in the InterPro and COG databases.
For this test, 30% of the pairwise comparisons and alignments were executed in 0.6 seconds at most; 60% were executed in 1.23 seconds at most; 90% were executed in 5.61 seconds at most and the 100% were executed in 4570.88 seconds at most.
Statistical evaluation of the concerted evolution hypothesis was obtained using a Shimodaria-Hasegawa test (SH, [ 78]), applied to alignment C; the test was executed using DNAml in the PHYLIP 3.65 package [ 79].
Whenever Sim4 failed to align cynomolgus monkey cDNA sequence with human genome DNA sequence, comparison by BLAST program was executed, and the alignment was corrected manually.
Before each pairwise comparison was executed, pairs of aligned sequences were extracted from the alignment file, placed in a Phylip format file and gapped positions were removed.
Indel Realign was executed using the full Smith Waterman alignment algorithm and base quality scores of reads were recalibrated in the aligned.BAM files.
The profile neighbor-joining algorithm was executed with 10000 bootstrap replicates on the RNA structural alignment, using the GTR model and rate matrix 'Q_ITS2.txt' for distance correction.
Second, another experiment was executed to observe the differences between the sequence alignments with different version of BLASTP.
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