Exact(1)
With the caveat that sometimes duplications could produce a merged sequence and uncertainty of donor assignment grew for shorter SDs, we have only interpreted this map for duplications involving long sequence and multiple subunits, i.e., at the top of the hierarchy.
Similar(59)
Sometimes the overlap of different sequences or contigs falls outside of the tolerance of assembly programs, and a manually merged sequence is needed.
Applying this merging approach to the simulated data set described above, but this time using both paired-end reads, we see a factor of 5 reduction in the error rate of all merged sequences (average error of 0.24% reduces to 0.05%; Additional File 1).
The tfs3 of strain B8 has one coding sequence less (HPP12_ virB-2) and a merged coding sequence HPB8_543 of which the first part corresponds to the coding sequence HPP12_1331 and the second part to the coding sequence HPP12_1332.
As an example, work out the -encoded merged sequence of the gaps in Table 5.7.
A pictorial example of this is shown in Figure 1, section Bi, in which the middle UTR state is used to allow the correct prediction of two genes on the same strand within a merged transcript sequence.
a NBS, R, and All genes means the merged sequence of NBS-LRR genes, non-NBS-LRR genes, and all the 11 genes, respectively, when calculation.
The merged sequence datasets were aligned to HIV-1 subtype B reference strain HXB2 (GenBank Accession No. K03455) using a modified NAP algorithm [40].
The subsequent annotation were all based on the merged sequence set.
When the two bases are identical, PEAR simply inserts this base into the corresponding position in the merged sequence and assigns the product of the quality scores: because errors are independent from each other (see Section 2.1).
Because the sequence of merging studies slightly influences the outcome of the consensus data set, in cases where computationally feasible, we merged the data calculating all possible merging sequences and selected the best sequence on the basis of the mean deviation of the merged sequence to each original data set.
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