This length of sequence conservation could be used to more effectively identify candidate genes using homology-based search tools.
For each combination we used the following equation: \sum _{m = 1}^{m = {\rm \#\ genes} - 1} \quad\sum _{n = m + 1}^{n = \#\ {\rm genes}} ({\rm Length(}X_m ) - {\rm Length}(X_n ))^2, Cons: The protein isoform combination that results in the best-conserved alignment, measured as percentage of amino acid identity over the length of the alignment (Conservation score).
After calculating all possible combinations, we applied different methods to select a single combination: Cons: The protein isoform combination that results in the best-conserved alignment, measured as percentage of amino acid identity over the length of the alignment (Conservation score).
The exon/intron structures were obtained using the online Gene Structure Display Server (GSDS: ) with either GenBank accession numbers, or both coding sequences (CDS) and genomic sequences [ 28]. Figure 1B provides a detailed illustration of the relative length of introns and conservation of the corresponding exon sequences within each of the OPR paralogues in plants.
To improve identification accuracy, the mtDNA annotations were compared with other plant mitochondrial genome annotations, and all differences in coding predictions were reassessed on the basis of the choice of the start codon, length of plant mtDNA conservation, and the presence of identical motifs.
Among these, a recent screen using Drosophila demonstrated that the best predictors of mutability are length and conservation of the protein (Cooper et al. 2010).
For phylogenetic analyses, only the 7-transmembrane region including intervening inter- and extra-cellular domains was included (330 amino acids), as it was difficult to ascertain homology of N- and C- termini due to sequence length variation and lack of conservation across genes.
A detailed illustration of the relative length of introns and of conservation of the corresponding exon sequence within each caleosin paralog is provided in Figure 2B.
DGP assigns a probability score using a decision tree model based on sequence properties i.e. protein length, phylogenetic extent, degree of conservation and paralogy [ 18].
Such refined alignments at the superfamily level can be found rarely and could be further used as reliable evolutionary models to probe various issues of conservation, length variation, structural and functional aspects of protein universe.
