The method described in this manuscript is applied to HIV but can be used on any sequence dataset.
We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model.
The gene finder Prodigal was used on DNA sequences of all genomes to eliminate biases in annotation quality and to standardize the genes found in all genomes [ 15].
Note: blastpgp can only be used on protein sequences and not nucleotides.
Finally it should be noted that, while all other options are currently restricted to human, option 5 can be used on DNA sequences from any organism.
Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known.
When used on the sequence containing the rs327 T allele, one set of MC sequences eliminated the bandshift (Fig. 4A).
RepeatMasker [ 43] was used on sequences for each of the three classes for each species in order to identify the content for repeat elements in the BESs.
Three predictors of intrinsic disorder were used on the protein sequences: PONDR® VSL2B, CH and CDF.
The primers used on the sequencing reactions were the same used on the amplification of the target fragments.
