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Notice that the estimates sequence { H ˆ k } k = 0 ∞ converges to a constant finite limit since lim k → ∞ Γ k = lim k → ∞ η k Γ 0 = 0 for 0 < η < 1 and, therefore, lim k → ∞ Δ k = 0 in Eq. (10), which makes all the patterns collapse to only one asymptotically.
This method is similar to CD-HIT, but instead of counting k-mers, FastBLAST estimates sequence identity from the multiple sequence alignment.
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Based on these estimates, sequencing depth estimations ranging from 57 to 66 × coverage were inferred.
The scale bar represents 5% estimated sequence divergence.
The scale bar indicates 5% estimated sequence divergence.
The scale bar represents 0.5% estimated sequence divergence Fig. 7 Neighbor-joining phylogenetic tree of AOB amoA gene sequences retrieved from the vegetable soil.
Like most of the DF schemes, the proposed scheme can be partitioned into two blocks: the decode block, where the information sequence is estimated; and the forward block, where the estimated sequence is encoded and forwarded.
To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).
Reads that were present more than 5× the estimated sequence depth were removed from the dataset.
With the assumption that most differences in RTS were caused by single nucleotide changes, the estimated sequence similarity was calculated for all genomes (Table 1).
However, if the estimated sequence gaps are added in, the estimated sizes are very similar.
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