For small sequence lengths, for example, and, we are able to use exhaustive search to verify that the solution obtained using ASA is globally optimal.
As this problem is not analytically tractable, even for small sequence lengths, it was solved numerically using MATLAB®.
Thereafter, artificial duplicates associated with pyrosequencing were removed using cd-hit-454 [ 30] at a threshold of 98%, and Seq-trim [ 31] was used to remove small sequences (length < 100 bp) or sequences with low quality (QV > 20, quality window = 10), as well as poly-A or poly-T tails, and adaptors.
In general, a smaller sequence length leads to a shorter run time in the computation of state transition matrices.
To test the near-optimality of the sequence obtained using the ASA, for smaller sequence lengths of and, we use exhaustive computer search to obtain the globally optimal S&H sequence.
While the Rieske domain is similar, differences are observed in the catalytic domain, which is smaller in sequence length than those described previously, yet possessing an active-site cavity of larger volume when compared to oxygenases with larger substrates.
G. aurea genome has a 2.4 times smaller total exonic sequence length, 4.0 times smaller total intronic sequence length, and 13.0 times smaller total intergenic sequence length, as compared to M. guttatus.
In practice, however, z is small, independent of sequence length and substitution probability.
In addition, Cummings et al. [ 12] analysed complete genomes and subsamples of them, concluding that small increases in sequence length will greatly increase the chance of finding the correct whole-genome tree when sequence lengths are below 3,000 base-pairs (bp).
