All of the elements included in the phylogenetic analysis as well as the subset of 28 annotated elements were used to define two new alignment profiles for each of the three characteristic domains of the DIRS1-like retrotransposons: reverse transcriptase, methyltransferase and tyrosine recombinase.
The alignment profile and the positive identification of a MazG domain by MotifScan, CDART and SMART, implies that these conserved regions encode key amino acid residues in the pyrophosphohydrolase, most likely the active site of the MazG protein.
We chose to be less stringent in the first step by using an alignment profile designed using a large diversity of elements, one third represented by other types of tyrosine recombinase-encoding retrotransposons as well as one Gypsy element.
A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc).. Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs) are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments.
The input to MAPGAPS is a set of alignment profiles, a consensus sequence for each profile, and a manually-curated template alignment of the consensus sequences.
Moreover, the spacing of the DDE catalytic residues does not align with that of other IS5 family members [ 5] and this would probably explain the difficulties to identify them based of alignment profiles search methods.
The slight skewing (non-symmetry beneath the peak) of the alignment profiles in Figure 6B indicates that siRNAs whose ends do not precisely coincide with the ends of P4R2 RNAs tend to be internal to P4R2 RNAs.
Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing.
Cyntenator (Roedelsperger and Dieterich, 2010) uses genes as markers and is based on a progressive alignment of profiles of gene-order data.
