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Zhao et al. [ 11] show that poor sequence coverage can be overcome by using multiple reference genomes, but problematic for this approach are major rearrangements in the genomic sequences of more distantly related species.
Genome annotation was conducted using multiple reference genomes, including 'Ca. L. asiaticus' (GenBank accession # CP001677) and other related microbial genome databases obtained from GenBank.
The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects.
The bias caused by the reference-guided variant discovery can now be solved by using multiple reference genomes (Gan et al. 2011).
At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are moving toward providing multiple reference genomes.
For pathogen identification, multiple reference genomes are usually available for a known pathogen and should only increase as whole genome sequence (WGS) data becomes easier to generate and analyze.
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Therefore, resequencing a segregating population can be used to improve multiple reference genome sequences.
The PREPACT 2.0 update now allows users to freely select from multiple organellar reference genomes for prediction of editing in their query sequences.
A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes.
And, as multiple high-quality reference genomes are developed, many more SNPs in the pan-rice genome should be discovered.
Our web application addresses and extends these requirements by combining different data types and including the reference genomes of multiple organisms by utilizing modern web programming technologies and components.
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