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In cases of alignment ambiguity, both alignments are shown below the logo.
To quantify the reproducibility of manual re-measurements of the CPT in cases of alignment errors, the intraclass correlation coefficient (ICC) was calculated.
The 70%_PERF_ALIGN threshold thus seems a good compromise between the number of conserved probesets and the fidelity of alignments, especially in cases of alignment drop due to intervening stop codons as found in the tomato GeneChip.
Similar(57)
The distribution and density of the electromagnetic flux, and variation of efficiency versus load level of the system and responses of the system in case of different alignment errors are also investigated and reported for both ideal operation conditions and in case of alignment errors.
The CPT measurements in case of alignment errors were highly reproducible between the two RCs with a κ value of 0.70 and an ICC of 0.92.
Similarly, in case of alignments to Su(HW) peaks, the region ranged halfway to the next peak.
In case of alignment-free discovery, the conservation of a motif is scored irrespective of its orientation or position within a promoter sequence.
The alignments of annotated genes and shotgun reads were used, in cases of large alignment depth, to assess the borders of a repeat unit.
More challenging scenarios arise in cases of gapped alignment of RNA-Seq reads, and with the presence of insertion or deletion of bases in the sequence of reads.
In cases of misalignment, alignments were corrected prior to subsequent phylogenetic analyses.
This file served as the input for Figure 3 ; in cases of multiple alignments per gene only one of them was used, others being labeled with a "no hive" flag.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com