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However, regardless of the methodology used for SNP discovery in tall fescue, the haplotype complexities created by the allohexaploid genome structure will still need to be addressed, and the approach taken in this study is applicable to data from multiple sequencing methodologies.
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Firstly, we have achieved a high average sequence coverage of the CPC98 mtDNA genome using Illumina GA (9.1×) and Sanger (7.9× in total, with data generated from between two and seven independent primary multiplex PCRs) sequencing methodologies generated from multiple independent DNA extracts.
All but the Global Ocean Sampling Expedition used similar shotgun sequencing methodologies.
Furthermore, new sequencing methodologies emerge.
Details of sequencing methodologies are included in the Methods.
Multiple sequence alignment is an essential methodology to study biological data, such as homology modeling, phylogenetic reconstruction and etc.
Finally, consensus DNA sequences for each repetitive element identified with either methodology were built from multiple sequence alignments with ClustalX [ 15].
In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations.
The methodology used here, namely the use of multiple sequence alignments to construct hidden Markov models (HMMs), means that the HMM does not distinguish orthologs and paralogs.
(The improvement expected from this methodology is analogous to the improvement from a multiple sequence alignment compared to a pairwise alignment).
Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome.
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