To address this, our model can also be used to investigate if the mutations observed at a given genome position are real, by simulating the number of mutations that would be expected from sequencing and sample processing error alone, and comparing this distribution to the observed number.
Subsequent cloning and heterologous expression in E. coli revealed that both proteins were covalent flavoproteins, as was expected from sequence analysis: both contained the distinguishing VAO family covalent-FAD motif (Fig. 1; Fraaije et al. 1998).
This rate is approximately 3 4 times higher than would be expected from the sequencing of DNA from a normal human diploid source [ 30].
Ussery et al. (2002) reported that in microbial eukaryotic chromosomes, the purine tracks occur more often than would be expected from random sequences, and are localized mainly in non-coding regions.
Purine stretches inside ORFs are known to block transcription via the formation of an intramolecular triple helix (Bidichandani et al. 1998; Grabczyk and Fishman 1995) while purine stretches were also reported to occur more often in fungal genomes than could be expected from random sequences (Ussery et al. 2002).
Furthermore, amino acid compositional similarities among mytilid species (or even between F-ORF sequences and protein-coding genes within a same genome) would not be expected from non protein-coding sequences since they are not subject to selective pressure to preserve protein structure and function [75].
The plots of the GC content of individual contigs showed in C. angaria and C. remanei (and to a lesser extent in C. sp. 11) a wider variation than other Caenorhabditis, with a range that would be expected from a combination of sequences from nematodes and high CG bacteria (Fig. 1A).
The length of the peptide sequences derived from the ESTs had to cover at least 80% of the peptide sequence length which can be expected from the corresponding part of the protein sequence from UniProt.
Our results indicate that Flowsim can be useful to estimate the quality of an assembly that can be expected from using Titanium to shotgun sequence a genome.
Finally, we used the EMSA to show that the Dbuz\ Galileo THAP domain binds to BS2 and BS3, as would be expected from the high degree of sequence conservation, particularly in the core region (Fig. 6D).
