Sentence examples for upstream alignment from inspiring English sources
Fixed parameters that had a significant increase on lane departure were horizontal curvature at the current segment, and the difference (max-min) in horizontal curvature within the 300-m adjacent upstream alignment.
Alt Event Finder relies on upstream alignment and isoform reconstruction tools.
Interestingly, more routine processes such as 'biosynthesis' and 'ribosome' turned out to be correlated with low upstream alignment scores (Table 1, 2, Additional file 1: Table 1).
In conjunction with upstream alignment and isoform reconstruction tools, we demonstrated that Alt Event Finder has the ability to identify novel cassette exon events that are not documented in the established databases.
A Spearman rank correlation test [ 26] was performed on each GO term vector and the upstream alignment score vector, in order to test whether each GO term is associated with high or low proximal upstream conservation.
To measure proximal promoter conservation, upstream alignment scores of human genes were computed by counting the number of matches in the alignment between the sequence 1 kb, 2 kb and 5 kb upstream of the transcription start site and its syntenic mouse sequence.
Figure 2 visualizes the upstream alignments of selected development genes with top alignment scores.
Another portion of MGC upstream alignments (293 loci) were removed as the upstream region fell within gap or repeat regions of the Btau4.0 assembly.
We used multi-species (human, chimp, dog, mouse, rat, chicken, zebrafish and fugu) upstream alignments downloaded from the UCSC genome browser (version May 2004) and extracted the human and dog alignment.
We identified functional categories that are enriched towards high proximal promoter conservation by computing a Spearman's rank correlation on upstream sequence alignment scores and Gene Ontology (GO) [ 11] terms.
We chose the 1000 bp upstream multiple alignment file (maf) for our analysis as proximal TFBSs tend to be found within 1000 bp of the transcription start site (TSS) of a gene [8].
