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The boundaries of putative TM helices or sheets tend to be predicted inaccurately and vary between different prediction methods.
The boundaries of putative cluster loci were identified by scanning for the location of the furthest piRNA sequence on either end of the locus.
The housekeeping genes and brain-specific genes showed similar association patterns with human-specific TF-binding sites, as measured by the number of binding events located within the boundaries of putative target gene-specific regulatory regions (table 2; fig. 4 and supplementary fig. S6, Supplementary Material online).
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We searched in the neighborhood of the hits, and found that in many cases there was (i) a sequence similar to the reverse complement of the genomic sequence identified by the hit (a putative TIR), and (ii) a TSD of 8 bp at the boundaries of these putative TIRs.
To define the boundaries of this putative region, we in vitro-translated a series of FOXP3 proteins that all retained the zinc-finger, leucine-zipper and FKH domains, but in which the N-terminus was truncated to varying extents (Figure 5A, 5B-bottom).
GeneFinder was used to delineate the exon boundaries of the putative genes.
Significant differences in the boundaries of the putative exons are interpreted as alternative splicing events.
Boundaries of the putative prophage regions were determined by a combination of checking homology with wPip and wCauB prophages and manual assessment of gene annotations in boundary regions.
A search using this statistic was conducted over different CNV lengths to find the position and length (in number of SNPs) that yielded the lowest probability, defining the boundaries of a putative CNV.
Automated base calling of the raw sequences for mapping of boundary ends of putative conserved miRNAs and removal of vector and adaptor sequences were performed with commercial software Sequencher 4.9.
In this way, 1448 contigs are predicted to contain a boundary of a putative HGT event (which would assume a minimum of 362 possible HGT events in the genome of E. coli since the same boundary will appear in four consecutive contigs).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com