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However, despite the decreasing costs of NGS technologies (Davey et al., 2011; Straub et al., 2012), financial constraints can still prevent the acquisition of higher-coverage WGS data or the use of multiple sequencing strategies.
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Our approach of using multiple high-throughput sequencing strategies resulted in high quality genome sequence that continuously covers the large majority of the S. arboricolus genome.
Degenerate primers based on conserved regions were designed by employing multiple sequence alignment strategy using ClustalW.
Therefore, integration of multiple sequencing platforms is one strategy for de novo sequencing when there is no reference genome available [ 32].
Any plant from a Mu-active family contains multiple new insertions and those insertion sites can be rapidly identified using high-throughput sequencing strategies.
Two sequencing strategies were adopted.
For target proteins with poor quality or sparse multiple sequence alignments, the appropriate strategy is to de-emphasize coevolution in favour of generic structural features, but where sufficient homologous sequences are available, the overwhelming value of coevolution is clear.
The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Our data also provide evidence that the rapid divergence of Ad7d to a novel genome type Ad7l could have been due to viral strategies involving multiple sequence changes in E4.
Moreover, using multiple sequence alignment and pairwise sequence alignment strategies, we showed that RbTrxR-3 has high overall sequence similarity to other teleostean TrxR-3 proteins, including highly conserved active site residues.
Recently, advanced methods have extended the profile strategy to considering multiple sequence information on both sides, target and template, to improve performance [15].
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