Sentence examples for matrix for motif from inspiring English sources

We then construct the similarity matrix for motif discovery.

The exact core segment and bilateral tolerant segments of HREs were obtained and formulated as a novel matrix for motif searching and evaluation.

The position-specific scoring matrix for this motif, which can be used to search custom datasets via the MAST option of the MEME server, is presented as Additional File 6.

This might be caused by the low specificity of the DnaA and GcrA matrices used for motif finding, but may also suggest that in some alpha-proteobacteria the DnaA->GcrA->CtrA circuit may be simplified by excluding GcrA.

GR ChIP-seq data identified peaks for GR binding that were examined using MEME [ 25], DNA motif finding tools, and presented a position weight matrix for the enriched GR motif and the co-occurring AP-1 motif.

Additional file 6 lists the adjacency matrices for the motifs that are identified in conditional networks, total number of conditions they are present and the number of conditions they appear significant.

This affinity can be modeled as a function of the log-odds score of the binding site, the ratio of the probability of the site under a position-specific model to the 'background' probability of the site (Stormo, 1998), and can be captured by a position-specific weight matrix (PWM) motif for the specific TF.

The position-dependent scoring matrix for the 14 bp motif was used as input to the MAST algorithm to search similar motifs in a 20 kb upstream region and in the first intron of 10 candidate genes, including ptc1, candidate genes were selected based on gene ontology associations, to cover a wide array of cellular and developmental processes.

The RSAT matrix-scan tool was used for motif scanning: 1st order Markov Model was used to generate the background model from the input sequences, and the sequence matches with the weight score > = 4 were retrieved [ 74].

More specifically, it uses position specific scoring matrices to search for motifs that specify transcription factor binding sites.

A simple similarity score between a motif and a weight matrix, i.e. the sum of the weights of the matrix for the letters of the aligned motif, was employed to relate the uncovered motifs to known TFs.