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In this benchmark dataset, each set of allele-specific data had been partitioned into five subsets with minimal sequence overlap.
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For a group of overlapping potential CRMs, we classified these CRMs into nested sets and took the minimal sequences in the nested sets as the representing CRMs (See Figure 2).
We then re-scored the mouse sequences using the T20 Cutoff Human Databases and found a striking reduction in the T20 scores for the full-length and framework only mouse sequences, with minimal overlap between human and mouse sequences.
The family tensions and action sequences overlap throughout the drama.
In order to cope with this, EmiR allows for a minimal 50% overlap on genomics positions of the sequence read and the miRNA loci for annotation of the sequence reads.
In the first step, 45 pairwise genome-wide reciprocal best-hit protein BLAST searches were performed on 10 genomes, using InParanoid [ 95] (configured as follows: two-pass BLAST, with bootstrapping, not using an outgroup, matrix BLOSUM45, minimal BLAST bit score 40, sequence overlap cut-off 0.5, segment coverage overlap 0.25).
The most common areas of loss and gain of DNA sequences and minimal regions of overlap are shown in Table 4 > -wrap-foot>.
Analyzed sequences overlapped those amplified in the qPCR assay.
SLC17A9 belongs to the major facilitator family of proteins SLC17 but has minimal overlap with peptide sequences of other members of this family that carry different peptide sequences like R-DE.
Contigs were assembled automatically using Sequencer™ using a minimal overlap of 17 nucleotides and a minimal identity of 85% and refined and corrected manually.
In order to handle variations in miRNA transcript lengths, a sequence read is annotated to a transcript locus from the annotation files when there is a minimal 50% overlap on genomics positions.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com