Sentence examples for background set of sequences from inspiring English sources

These sequences were used as pair-weighted background to analyze the frequency of TFBS around insertion sites by the Clover program, which screens DNA sequence sets against a precompiled library of motifs and provides statistically significant over- or under-representation compared to a background set of sequences [34].

As over-representation analysis is designed to report TFBS predictions that exist to a greater extent in a set of chosen sequences than in a background set of sequences, we examined the effect of GC composition on motif enrichment scoring using backgrounds with varying GC content (i.e., high, low, and neutral GC composition) against several ChIP-Seq datasets.

This could be explained by the proportion of promoters containing a TATA-box in the background set of sequences, or by the relatively low complexity of TATA-box motifs which makes them hard to discriminate from background, particularly if we take into account the fact that promoter sequences are generally A/T rich [ 33].

For each motif, the number of matches was compared between a foreground set of intergenic sequences (adjacent to the N genes within the co-expression network) and a background set of intergenic sequences (adjacent to genes with detectable expression in the candidate cell type excluding sequences adjacent to the N genes within the co-expression network).

Enrichment of TFBS was analyzed among a target and a background set of upstream sequences using two different statistical tests.

We used a background set of promoter sequences extracted in a similar manner from the 'all genes expressed' present/absent call in skeletal muscle from this array technology [ 24, 27].

Background sets of promoter sequences (500 bp upstream of annotated mRNAs) from Arabidopsis, soybean and rice sequences were retrieved using BioPerl and genome annotation data available for each species in generic feature format (GFF).

We used the Weeder algorithm11 to identify the 50 highest scoring 'sequence words' between −2 kb and +0.5 kb of transcription start sites relative to a background set of approximately 26,000 human promoter sequences (Table S2).

As background set, 10 000 sequences of length 2121 bp with random genomic start positions were used.

For some foreground sets, extreme composition properties can make it difficult to obtain composition-matched background sets of comparable size from the associated control dataset, let alone a background with 2-fold or more sequences.

To take into account the base composition of the promoters a background model from a relevant set of sequences is estimated.