Briefly, for each probe, a 600 bp flanking window was formed, and a MATscore was computed as TM y), where n was the number of data points in the window, and TM y) was the trimmed mean of the background corrected probe intensities within the window.
Additional constraints were a maximum of one other SNP in a 100 bp flanking window and that the SNP must be located 50 bp from areas identified as indels by the pipeline [maq.pl SNPfilter -d 20 -n 20 -Q 60 -q 30 -w 50 -N 2 -W100 -f cns.indelse -F cns.indelpe cns.snp].
Genome-wide SNP data from a reference panel (1000 Genomes, v3 phase1)64 was annotated to NCBI Build 37.3 gene locations using a symmetric 100 kb flanking window, and both files were downloaded from http://ctglab.nl/software/magma.
Including 10 kb flanking window reduces the amount of sequence to 14%; focusing on annotated regulatory elements reduces it further.
We tested both types of data integration, with the size of the flanking window set to 100bp in the second type of integration.
We quantified the expression of bidirectional loci for each strand and 200 bp flanking window in each sample separately by counting the CAGE tags whose 5′ ends were located within these windows.
A similar pair of pinnacles top the main gable, flanking a window of unusual design; a bracket projects from the lower lobe to support a statue (no longer present), possibly of the Virgin Mary, to whom the priory was dedicated.
One of the bedrooms has original built-in armoires flanking a window.
Flanking a window in the small chapel-like final gallery of the Dia show, this painting faces a shimmering charcoal painting from 1967 titled "Deny II," in which the ellipses are larger, like Mr. Poons's paintings from the same time and shrouded in a hazy chevron, like Mr. Noland's.
Next, each aligned sequence plus 100 bp flanking windows were put into SRNALOOP a hairpin prediction tool [ 64].
"I can walk down a street and hear them say, 'Psst, I'm over here.' " To many a New Yorker's eye, the sculptures — perched above doorways, flanking windows or topping off columns — often simply go unnoticed.
