The absence of sequence context on one side of these polymorphisms further hampers the alignment of additional reads to form deep sequence clusters meeting the minimum allele count constraint applied during SNP detection.
In subunit β2, one non-synonymous SNP (nsSNP) was found at the N terminal signal peptide and involved an alteration of F and S residue at position 12 (aa numbering as in alignment of Additional file 6: Figure S3) and two others, D/E and N/T at positions 400 and 426, were found between transmembrane domain TM3 and TM4.
This process involved the identification, based on congruous BAC end sequence alignments, of additional BAC clones that confirm the CD, and is illustrated in Figure 2.
Such efforts would greatly benefit from software that could allow the simultaneous visualization on multiple alignments of additional predicted sequence features such as disordered regions, tm segments [ 87], coiled-coils, and low-complexity segments.
In contrast, when we used either the rsid or our alignment of orthologues (Additional File 1: Fig S1) as input for SIFT (Ng and Henikoff, 2001), the prediction was both "tolerated" with scores 0.45 and 0.50, respectively (score threshold <0.05 for "deleterious").
This was located between position 253 and 316 of the alignment of 183 CIRs (Additional file 7a).
We collected a representative set of putative viral, bacterial, archaeal and eukaryotic bacteriorhodopsins and constructed a multiple alignment of these sequences (Additional file 1).
The alignment of Alu sequences (Additional file 2) showed that this motif existed in all the predicted sequences of more than 200 nt.
As demonstrated by the multiple alignment of DsbA in Additional file 1: Figure S2, these proteins may only be found in prokaryotic, unicellular, plant, fungi, and invertebrate organisms.
A multiple alignment of gene sequences (Additional File 1) revealed polymorphisms shared between PPR-1 or PPR-2 and the genes from the D81Rfo sequence.
Whereas functional sequences were all of the same length (a full NAT ORF of 870 bp), pseudogene sequences displayed considerable length variation due to the significant number of indels disrupting NAT ORF (ranging from 865 bp for Colobus guereza NATP to 881 bp for Gorilla gorilla NATP), resulting in a multiple alignment of 890 sites (Additional file 5).
