The observed low-complexity sequences include both single amino acid repeats and repetitions of few amino acids.
The dominance of Asparagine in SSPs of species of low GC mirrors the trend observed in the low complexity sequences of Plasmodium falciparum, an AT rich species [ 32] and points to an early tendency of abundance of Asparagine in simple sequences.
We also observed that using the low complexity filtering option [31] did not alter significantly our results.
For the 2 and 5.5 Mbps channels, we observe that low-complexity hierarchical and hidden Markov models cannot characterize the bit-error processes, and consequently high-order full-state Markov chains are employed for accurate channel characterization.
The promoter sequences identified contained repeat sequences (e.g. ALU, L1) and simple repeats with low complexity, as observed in intron sequences.
Although isolated, short regions of repeated amino acids are observed in some Arabidopsis and rice Puf proteins, extensive stretches of low complexity sequence are not observed in these proteins.
Here, we find a high abundance of low complexity kmers, indicative of homopolymer problems, as observed in Jain et al.
Interestingly, we and others ([ 22, 27]; our unpublished results) have observed that there is a strong selection against low complexity inserts within core secondary elements of secondary structures of P. falciparum proteins.
There was no evidence for any major rearrangement although small gaps were observed due to differences in assemblies, likely the result of repeats or low complexity regions that are hard to assemble.
The Nimblegen probes contain almost no low complexity DNA on the array (Fig. 4c), but we observed that the regions of low coverage contain much more low complexity DNA compared to the regions with the good coverage (Fig. 4d).
It is observed that the determinant-based scheduling algorithm has the shortest run time among the low complexity scheduling algorithms.
