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Checking for overlap with the Phytozome annotation revealed that 7674 transcripts at 6063 loci were unannotated.
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The BLAT results for the BRENDA dataset were checked for overlap with the cluster dataset.
The RNA annotations from the pipeline were checked for overlap with the small RNA library.
The initial statements were reviewed and refined over three iterations by two researchers and checked for overlap with other statements and against the verbatim data.
The seed regions were checked for overlap with other known miRNA and miRNA* sequences and the targetscanS algorithm was used to predict miRNA*-mRNA pairs, if the seed sequence was previously unreported.
Those 295 hotspots are used to check for overlapping with the results of mediation analysis.
Therefore all identified ZFs/ZFPs subsequently were checked for overlaps with other protein motifs by manual inspection with Pfam and SMART [ 42] search tools and by BLAST search [ 43].
Genomic coordinates for all the nondubious ORFs in the SGD data set were extracted and checked for overlaps with the positions of the intermarker intervals in the recombination data set (Mancera et al. 2008).
For reasons of performance, intervals are initially sampled without checking for overlap.
For the presence of Pol II peaks near TSS's, we checked for overlap of MACS-derived peaks with a TSS interval file containing all annotated TSS-centered 500 bp intervals with overlapping intervals merged, having excluded TSS's derived from short gene transcripts (unprocessed transcript length ≤1 kb).
We checked for overlap between factors by estimating inter-scale correlations using Pearsons' correlation coefficient.
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