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Considering that the sequence analysis carried out here strongly suggests functional differences between the two sub-types, the expression of both sub-families may indicate that A and B-type CIRs provide complementary but non-overlapping roles at different stages during infection.
Figure 3A shows the alignment of predicted attC sites; we focused on the core domains of the attC sites for the alignment, considering that the sequence conservation in attC sites is restricted to two triplets (AAC and GTT) located in the R" and R' boxes [ 1].
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Considering that the sequencing error rate in ESTs was estimated to be about 0.0044 per base pair [24], there would be about one false positive SNP in a 227-bp EST.
In addition, considering that the sequenced RNA sample is polyadenylated, these results also suggest constitutive RNA maturation.
Considering that the sequences were all generated from a random shotgun library and sequenced to relatively low redundancy, it is unlikely that several sequences would be derived from the same location.
Considering that the sequences identified by PILER-DF are isolated and unique, it is possible to state that those sequences represent different transposition states of the same TE family, allowing for evolutionary or dynamical analysis.
This is not surprising considering that the sequences are anchored at the TSS in this analysis, and position dependencies between interacting motif-binding proteins are expected to be more relevant for short distances [ 36, 37].
Considering that the sequences are generated from a random shotgun library and that similar coverage of each genome sequence was used for analysis, these results suggest that the H. lacusprofundi genome contains the highest number of IS sequences homologous to H. sp. NRC-1.
With the observed base quality drop towards the read's end and considering that the sequencing data were obtained from a different strain then the sequenced one, we used less stringent conditions for alignment scores and filtered reads based on mapping quality parameters.
Also, consider that the sequence X→B appears 40 times and that X→C appears 10 times.
The condition (A5) is easy, for example, we consider that the sequence gamma_{n}=left { textstylebegin{array}l@{quad}l} frac{1}{n^{alpha}}, & nneq0, 1, & n=0,end{array}displaystyle right.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com