Sentence examples for searching upstream from inspiring English sources

DOI: http://dx.doi.org/10.7554/eLife.06885.003 By searching upstream sequences of the transcription start sites (TSS) of all three mouse miR-9 genes, we identified a putative Ngn1 binding site containing the E-box element CATATG located 2.5 kb upstream of the miR-9-2 TSS.

If those two entities did not specify specific permissions for the target statement, then those are searched upstream (Figure 4) until reaching the Project or even Deployment level.

Users can search upstream, downstream, or in both directions.

We searched upstream of the major Geobacter che operons and fliC loci for evidence of σ-regulated expression.

Furthermore, to obtain additional evidence for encoded proteins within the new intergenic transcripts, a RBS was searched upstream of the longest predicted open reading frame.

To investigate if the genes encoding these up-regulated proteins are potential transcription targets of Yap1p, we have searched upstream of each nucleotide sequence for the predicted Yap1p-binding sites [ 14- 16].

The preliminary motif definitions from the High Confidence and Expanded sets were used to search upstream of all 17,797 P. infestans genes, and the resulting matches were used to establish position-specific probability matrices (PSPMs; provided in Additional file 1).

Each PSPM was developed from matches within 200 nt of the translation start site, and then used to search upstream of each gene's start codon using the FIMO program [ 20].

For estimating motif frequencies, we searched upstream from start codons, and estimated false discovery rates using same datasets randomized by three rounds of DNA shuffling using shuffleseq in EMBOSS or Shuffle DNA (http://www.bioinformatics.org).org

Searching the upstream regions of genes for the PhoP consensus sequences can help us identify the candidate targets regulated directly by the PhoP.

Decreased search stringency may lead to false positives, but by including the proximate Oct-1 binding site and searching the upstream Atlantic salmon and human promoters at low stringency, without finding any adjacent CREB and Oct-1 motifs, we believe that the in silico predictions are reliable.