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In terms of our general results, elephants and the manatee were found to contain the most diverse sequences, while hyrax showed comparatively less diversity.
For the generation of phylogenetic trees, the most diverse sequences of each subgroup were aligned with ClustalW [ 18].
In contrast, Group III encompasses the most diverse sequences, probably due more than one U3 version being represented.
The resulting multiple sequence alignment was filtered so as to keep the 100 most diverse sequences and was converted into a Hidden-Markov Model profile using the HHsuite programs [ 32] integrating the secondary structure prediction from Psi-pred [ 33].
We attempted to establish this by using the N-terminal region (which is clearly shared between all dystrophins, dystrobrevins and dystrotelins) to perform a phylogenetic analysis against our most diverse sequences.
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Variants of the histone H2A family (the largest among histone classes family) are the most diverse in sequence and exhibit distinct functions, comprising DNA damage repair, transcriptional regulation, cell cycle control, and chromatin condensation [ 62], [ 63].
Thus, given the fact that the hinge region within aPKCs contains the most diverse nucleotide sequence it is interesting to observe that both isoforms contain information related to isoform-specific, distinct, subcellular localization in this region.
Although the high throughput achieved with fTEFAP, uncovered the most diverse array of sequences, there was little overlap between the taxa amplified with ENDOITS forward and reverse primers (Figure 1, green) and the 58A1F and NLB4 primers (Figure 1, red).
We also apply the "most diverse" method to sequences of European ancestry from the 1000 Genomes Project.
To determine the conserved motif of DUF4123, the 100 most diverse amino acid sequences were retrieved from the NCBI conserved domain database (Marchler-Bauer et al, 2013).
In addition to determining the full-length sequence of the most diverse isolates of variola virus, sequencing has been completed for >30 genes encoding various proteins from the other 37 isolates examined from the collection.
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