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The determination of phage relatedness is not based exclusively on sequence similarity but also takes genome organisation into consideration [ 15].
We report PiType, a novel technique for classifying protein interactions into obligate/non-obligate as well as into SP/ME based exclusively on sequence and network information.
Our results therefore show that the reconstruction of the phylogeny of the URR based exclusively on sequence alignments does not provide stable topologies.
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Also, the calibration used for BK-o is not a general eukaryotic calibration but one based exclusively on eukaryote sequences derived from eubacteria.
It is evident that the assignment of transcript orthology relationships based exclusively on reciprocal sequence similarity can produce misleading results if structurally different isoforms are inadvertently considered.
Analysis of the gene coverage using reads mapping to unique locations of the B. taurus reference genome based exclusively on sense strand sequence information, showed that of the 25,669 annotated B. taurus genes, 15,422 genes (60.1%) had at least one sequence read count (i.e. one mapped read) in at least one library.
In 1996, a third phylum, Korarchaeota, was proposed based exclusively on environmental DNA sequences, then, following another six year period, it was proposed that Nanoarchaea deserved a phylum designation of its own [ 29, 30].
Intriguingly, the phylogenetic analysis of Bingle and coworkers [ 14], based exclusively on IglA and IglB sequences, showed that Francisella sequences clustered together in a deep branch of the tree, and our approach did not identify any T6SS locus in Francisella.
New technologies and approaches are pushing S. cerevisiae annotation past the limits of a system based exclusively on a single reference sequence.
New technologies and approaches are now pushing S. cerevisiae annotation past the limits of a system based exclusively on a single reference sequence.
The previous report was based exclusively on maternally inherited chloroplast genome sequences (cpDNA) [ 24, 25] and thus it was unable to account for introgression, reticulation, and polyploidy [ 26- 28].
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