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We learned the Z-scores rather than PWMs because Z-scores reflect binding affinity (Berger et al., 2006), whereas PWMs often fail to capture detailed binding activity (Benos et al., 2002; Chen et al., 2007) and cannot be aligned with confidence for many homeodomains (Berger et al., 2008), complicating direct comparisons.
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These comparisons show that most of the A. thaliana mitochondrial sequence cannot be aligned with genomes outside the Brassicales.
They were not included in Fig. 1 because their sequences could not be aligned with confidence.
Nonhomologous insertions and sequence characters that could not be aligned with confidence were removed manually.
Nonhomologous insertions and sequence characters that could not be aligned with confidence were manually removed.
Typically, phylogenetic reconstruction is suited for analyzing subsets of homologous genes that can be aligned with confidence.
Approximately 90% (9,087) of the 10,171 human TSS regions could be aligned with confidence, and 61% (5,529) of them were with CGI.
Only sequence positions that are aligned with confidence are retained for model construction.
The last peptide (VVTVSLPR) cannot be aligned well with the deduced amino acid sequence for SAP98 (fig. 1 B).
Reads that cannot be aligned are optionally discarded.
However, the full precursor sequences cannot be aligned convincingly.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com