By use of a special paddle alignment scheme we are able to eliminate any bulk optic wave plates and polarization maintaining fibers in the interferometer and detection paths while preserving the advantages of a single input state system that illuminates the sample with circularly polarized light.
The nucleotide sequences were aligned and compared with those of known HPV types available through the GenBank database (http://www.ncbi.nlm.nih.gov/) by use of the CLUSTAL W multiple sequence alignment program.
The non-redundant sequences of each protein from both the animal and human hosts of the virus are then merged for a co-alignment by use of a local copy of MAFFT (obtained from http://mafft.cbrc.jp/alignment/software/); MAFFT is one of the most accurate multiple sequence alignment methods currently available [ 14].
Whole genome alignment was made by use of MAUVE and MUMmer program.
Intraoperatively, mechanical axis alignment was determined by use of a grid plate with radio-opaque straight lines, which was placed underneath the patient on a radiolucent table.
Multiple alignments were obtained by use of the ClustalW or ClustalX programs (Version 1.83) [ 68].
Thus, use of cross-species conservation data, within an integrative framework significantly (p<0.05, by FET) improved recall rate, and joint use of alignment- and pattern-discovery-based approaches yielded an additional statistically significantly improvement (p<0.05, by FET) over either method in isolation.
Sequences have been deposited at the EMBL databank with accession numbers presented in Additional file 3. The mitochondrial cyt b, and the two nuclear exons (IRBP and vWF) were aligned by hand with the ED editor of the software MUST [ 61] by making use of codon alignment (indels were always in multiples of three base pairs long).
To this end, we have designed SymSSP, an algorithm that post-processes the predicted secondary structure of all sequences in a multiple sequence alignment by (i) making use of the alignment's evolutionary information and (ii) re-introducing most of the information that would otherwise be lost.
In the case of the third fragment (281048), the missing region was identified by the use of translated alignments against the Ciona genomic regions where the missing region was expected to be found based on alignment with the human orthologous protein.
