ClustalOmega was used to align the sequences.
To this end, we multiply aligned the sequence of each HERV element with its partner and the full-length consensus HERV-H sequence from RepBase [ 25].
Hence, to examine the methylation pattern of the newly integrated Alu elements, we aligned the sequences generated in this study for nineteen of such Alu elements with their bisulfite converted sequences from our previous studies [ 31, 32] (Additional File 3, Figure S1).
INS collected and aligned the sequences.
To facilitate the presentation of sequence elements that characterize each group of proteins, the sequences of several representative proteins were aligned.
> -wrap-foot> The 23 experimentally determined TSSs were aligned and the sequences immediately 5′ to them were examined for nucleotide patterns that could comprise promoter elements.
In most cases, GC boxes in eutherian mammals were not consistently aligned to any particular sequence element, but instead appeared to arise de novo from nonfunctional DNA.
For each structure in our set of 328 membrane protein alignments, every time a structure residue ' a' in environment E has a corresponding residue ' b' in one of the aligned sequences, the matrix element A E ba is increased by unity.
Moreover, we looked for the I element promoter in the D. mojavensis copies by aligning the flanking sequences of each copy with the promoter sequence of the I element of D. melanogaster (Minchiotti et al. 1997; Han 2010).
To get insights on the genetic diversity of the DIRS1-like elements found, we aligned the partial sequences of the pol region that we obtained.
Zebrafish sequence elements phox2b-ZCS-8.3, phox2b-ZCS-16.6 and phox2b-ZCS-20.1 phox2b-ZCS-20.1 phox2b-ZCS-20.1s PHOX2B-HCS-73.5, PHOX2B-HCS-108.3 alignedX2B-HCS-114.8, respectively.
