On both genomes for which alignments were studied, the chimer rate dropped when the S1 (Sanger mates) set was included.
We first grouped sequences by higher taxa (i.e. Amphisbaenia, Anguimorpha, Gekkota, Iguania, Scincomorpha, and Serpentes, though these are not all monophyletic as previously defined), for which alignments were relatively straightforward under the default MUSCLE parameters.
We found that all five of the hot spot central regions for which alignments are possible contain differences within sequences 14 bp or longer consisting of more than 80% poly-pu/py and at least 50% G/C (Table 2).
We estimated the polymorphism of P. vivax and the genetic divergences between P. vivax and each of the two nonhuman primate parasites, P. cynomolgi and P. knowlesi, on the 4,300 shared genes for which alignments were carefully curated, out of which only 2,492 genes have known products.
For read pairs in which alignment was still not found for both reads, the reads were trimmed to 50 bp and aligned using '-n 0' again.
Dermal fibroblasts align to grooves as shallow as 35 nm if cultured for sufficient time, below which alignment of cells no longer appears to exist [31].
We analyze the alignments of structure pairs for which rigid alignment methods returned short alignments as compared to the length of the smaller protein.
Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd.
In the third step (table 3), we divided the sequences by the quality of alignment into those for which the alignment was judged to be unambiguous by the HoT methodology (Landan and Graur 2007) and those that contained alignment ambiguities.
