Sentence examples for matrices to scan from inspiring English sources

The mast program uses the resulting position-specific scoring matrices to scan BCL2DB sequences for BH motifs.

Thus, we can use one of the two matrices to scan the sequences potentially containing TFBSs to discover them [ 10].

Software such as the MEME suite [ 27] and MOODS [ 28] can use these matrices to scan new sequences for regions that match the PWM, typically using a certain score threshold to call a site.

We used such a matrix to scan all genomes considered in this work (see Additional File 1, Table S1 for all organisms list) with a sliding window approach and a scoring function from Schneider and collaborators (1986) [ 62]: Si = (1/L) Σj [2 + log2(Fij)], where Fij is the frequency of base i at position j of the L-mer.

The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome.

PWM1, PWM2 and PWM3 matrices were used individually to scan entire genome sequences, one nucleotide at a time, by a sliding window method as described previously [31].

These matrices can be used to scan genome sequences for matches to the TF-binding motif.

The resulting scoring matrices were then used to scan genomic sequences (excluding known protein-coding stretches) from all species studied individually, and on both forward and reverse strands.

ChIP data have been used to compile position-weight matrices, which were used to scan the genome for TF-specific binding motifs (Dunham et al., 2012; Kranz, et al., 2011) independent of the cellular context.

The Neural Network Promoter Prediction v.2.2 [68], TRES – Transcription Regulatory Element Search, which performs searches within the TRANSFAC database [69] and the PromScan program, that generates an alignment of known sequences and matrix frequency [70], were used to scan DNA sequences for potential binding sites.

Subjects were instructed to scan the matrix as fast as possible from the top left to the bottom right and to decide whether or not the matrix contained a target stimulus by pressing either a left ("yes") or right ("no") response key.