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Branch length estimation was critical for comparative analyses in this study, so the genetic dataset required unambiguous genetic alignments and the maximum gene coverage of the species analysed.
By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
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Biclustering was performed using default parameters except as follows: amount of overlap allowed (50%), gene coverage (set to cover all genes) and the number of genes expected (set to maximum number of genes in the data set).
The gene coverage.
Gene coverage density plot.
Cell coverage is calculated in the same way of gene coverage or condition coverage.
(4) Two types of gene coverage were calculated: 'total coverage' and 'adjusted coverage'.
In this step, we also computed other information, such as query coverage, subject coverage, and gene coverage.
We want to achieve maximum coverage of rice genes, and thus combined the resources, but do not believe that the occurrence of the same GO annotation in multiple resources indicates a greater likelihood of that annotation being correct.
To identify RNase HI, HII, and HIII coding sequences in a genome, two strategies (a remote homology search and a protein domain search) were applied to ensure maximum coverage of the genes (See Methods).
Maximum television coverage should be sought, especially by Al Jazeera, as individual Iraqis relate their stories.
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