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During cross-validation, a model is trained on all but one alignment from the training corpus and testing is performed on the withheld data.
One alignment was based on 16,636 nt positions of the complete mitochondrial genome, except for the highly variable ETAS (extended termination associated sequence) domain within CR.
This excludes contributions from the other crystalline peaks, putting too much emphasis on the contribution from one alignment of the cellulose crystal lattice.
Any combination of the character states in the aligned sequences at one alignment column represents a so-called character[ 3], which is sometimes also called site pattern[ 4].
Each set of protein sequences were aligned individually, then concatenated as one alignment.
To increase specificity, DELLY only applies this k-mer counting to one alignment direction, forward or reverse strand, depending on the paired-end induced alignment direction.
However, when aligned to each of the 17 sequences, only one alignment resulted in a Z-score of 4 and all the other z-scores were ≤2.
One alignment contained all annotated loci with 15,865 bp (coding genes, l-rRNA, s-rRNA, replication origin, tRNAs) and thus excluded only 487 bp of non-annotated loci.
PASA per default supports only one alignment per EST/transcript.
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One alignment-free method is the Regulatory Region Score (RRS) proposed by Koohy et al. [ 15].
To reduce computational intensity, identical reads were merged together, and sequence similarity was detected using one-to-one alignment by BLAT [ 51] (-tileSize = 10 -stepSize = 5).
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