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The study is also the first published analysis of multiple whole genomes of the same cancer, reflecting continuing advances in sequencing technologies and the ability to analyze whole-genome data.
For gaps or insertions of one nucleotide that were identified in multiple whole genomes, the type (missing or extra nucleotide) and length of the homopolymer were assessed based on a majority wins rule.
The increasing availability of sequences and the now common need to align multiple whole genomes has repeatedly pushed each of these homology search algorithms to the point where they are no longer viable, demanding the development of software that takes advantage of new technologies and novel algorithms with refined heuristics.
PanArray employs a greedy probe selection algorithm to tile multiple whole genomes using a minimal number of probes.
In this article, we present a new whole-genome alignment tool, named Mugsy, which can rapidly align DNA from multiple whole genomes on a single computer.
There are a number of whole-genome alignment tools that can align multiple whole genomes (Blanchette et al., 2004; Darling et al., 2004; Dubchak et al., 2009; Hohl et al., 2002; Paten et al., 2008).
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A multiple whole genome alignment of all Cpn clinical isolates served as backbone for comparative genomics.
Position-specific conservation scores were derived from multiple whole genome sequence alignments between the human and 16 other vertebrate genomes [25], [32].
Furthermore, the integration of data sets from multiple whole genome platforms is complicated by the interrelated nature of the genetic and epigenetic signatures that characterize individual cells in both their normal or tumourigenic states [12].
Third, as mentioned above, part of the progressive diversification of RBR genes most likely has been associated to the multiple whole genome duplications that occurred in higher plant lineages.
As multiple whole genome transcriptomic studies aiming at identifying genes and pathways explaining variation in similar traits become available, it becomes possible to evaluate the repeatability of changes in transcriptomic patterns across studies.
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