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Five of the phages did not yield DNA amplicons with any of the primer combinations tested (ϕ1, ϕ4, ϕ7, ϕ12 and ϕ16), either due to gene absence, sequence divergence or DNA modifications that prevent efficient PCR amplification [ 36, 37].
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Thirteen LTR sequences were 5' junctions and sixteen were 3', based on the complete absence of sequence similarity beyond the 5' or 3' ends, respectively, of the aligned LTR sequences.
Absence of sequence coverage at the position of an SNP in one or two of the sequences is denoted in Table S3.
Among the 21 probes, 2 probes are shared by more than one species due to low or absence of sequence variability, i.e. Rpam for Rhizopus azygosporus/Rhizopus microsporus and Fumop for Fusarium moniliforme/Fusarium oxysporum/Fusarium pallidoroseum.
These functional components (moves, steps or strategies) can be identified for each genre and such knowledge (e.g., presence, absence, and sequence of components) can then be used in the context of ESP instruction.
On one hand, sometimes functional orthology exists even in the absence of sequence orthology and vice versa.
In the absence of sequence information, methods for identifying peptides include the use of de novo computational tools, as well as the use of trans-species comparisons or near neighbor genome sequences [1], [2].
This absence of sequence information would tend to cause an overestimation of the false positive rate.
Nevertheless, the identification of evolutionary novelties requires also the absence of sequence conservation in related species.
However, the absence of sequence data from the latter prevents establishment of any phylogenetic relationship.
Another important feature of PPKL is Pro to Thr substitution in the conserved SAPNY motif and the absence of sequence similarity in the B12-B13 okacid-bindinginding loop.
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