BACs overlapping the chromosomal inversion breakpoints (as indicated by the alignment of the two BES of each BAC, inside and outside the inverted region, within a distance <300,000 bp) were filtered, and the orientation of both BESs relative to the O. glaberrima S1 genomic region was analyzed.
For example, if the nucleotides in the region s i appear in an alignment with a known protein, a 'protein alignment' feature will score positively if the associated label t i represents a coding region in the frame/strand indicated by the alignment.
As indicated by the alignments, the rif cluster appears to be inserted between two genes encoding a conserved hypothetical protein (AMED_0612) and the unique DNA-directed RNA polymerase β subunit (RpoB, AMED_0656).
Resistances to single antibiotics were also indicated by sequence alignment of the AMR-related probe set to the genomes.
One of these splice sites might be located in the pore region of the channel as indicated by sequence alignment with other better characterized TRP channels.
The new change in TIMM44 C925A maps to exon 9, and corresponds to a nonconservative missense substitution, P308Q, in a highly conserved position, as indicated by clustal alignment with the orthologue proteins from different species.
Confirmed Class 1 events mapped to genic regions in 78.9% of cases, as indicated by their alignment to sequences in either our intronic or exonic sequences database (table 5).
Finally, conserved domains, as indicated by alignment strength and HC amino acids are boxed and the alignment of these conserved domains from representative organisms is shown in Figures 2, 3, 4. Multiple alignment analysis of Trs120-related proteins is shown in Figures 2 and S1.
What tracker considers to be multiple footprints may correspond to a single potential ncRNA gene, as indicated by alignment of the region between Hoxd-11 and Hoxd-10 with the corresponding ESTs (not shown).
The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes.
