Sentence examples for background sequence for each from inspiring English sources

To assess the statistical significance of overrepresented 8-mers, we generated a 10 kb background sequence for each cluster.

The seed sequences are required to remain in their assigned subgroups while the sampler iteratively reassigns the remaining sequences to subgroups and adds or removes pattern residues with probability proportional to the degree to which the evolving patterns distinguish the foreground from the background sequences for each category.

A background sequence for a particular binding site is generated of length equal to that of its upstream region (up to 600 bps).

Background sequences for these datasets were constructed using synthetic data, altering the probability of choosing each nucleotide to reflect the species GC-content as required.

Background sequences for the E. coli datasets were created as above.

Background sequences for other species were created by randomly choosing nucleotides, altering the weighting to reflect GC-content as required.

As background sequences for DREME, Amadeus and Trawler, we use 1, 5 and 10 dinucleotide-shuffled copies, respectively, of the foreground sequences.

Motif width was set to be 10 for both software, and the background sequences for DME were the promoters of non-RPGs.

We collected the background sequences for CREB, SRF, TBP, MEF2 and MYOD datasets from public databases (e.g., http://www.ncbi.nlm.nih.gov and http://www.ebi.ac.uk) as the respective sequence backgrounds.

The motif visualization program MotifViz [ 19] was used to detect the transcription factor binding sites with motif match p-value cutoff 0.01 and with all intergenic sequences of S. pombe and S. japonicus as background sequences for searching with the respective species.

For each method, the parameter setup was adopted from [ 21] except that no background sequence information was used for BioProspector.