Sentence examples for background frequency for each from inspiring English sources

A HMM profile specifies a probability distribution over the alphabet of the 20 common amino acids, taking into consideration the background frequency for each amino acid, computed by counting amino acid occurrences in all known proteins, or only in the proteins of the family under consideration [25],[25].

We demonstrate how to test the statistical significance of the motifs discovered via the graph pruning/mathematical programming approach by using the background frequencies for each base or amino acid and computing the motif scores' probability distribution [ 38].

Taking all peptides within the source proteins as the background, it was found that the predicted background frequency for glycosylation for the training set was 9.11% (29654 peptides out of 325276) and for the test set 10.7% (47958 peptides out of 447453).

The PSSM scores for any column all take the form (ln R i )/λ, where R i is the ratio of target to background frequency for residue i, and λ is a scaling factor [ 23].

The matching score between X and Y is computed using the following equations: M (X, Y ) = ∑ i σ (x i, y i )   and σ (a, b ) = { 1 + log ⁡ 4 (0.25 / p a ) if     a = b log ⁡ 4 (0.25 / p a p b ) otherwise where p a is the background frequency for base a in the input sequences or in the whole genome.

The sequence present on the promoter array was used to assess the background frequency of each E-box motif.

Using the reference structural dataset as a source for amino acid frequencies and contacts, we estimated a log-odds contact matrix by measuring the ratio between the frequency of each possible contact and its expectation given the background frequency of each single amino acid.

The frequencies are further converted into odds scores by dividing the observed frequency by expected frequency or the background frequency of each nucleotide at each position, averaged over the proximal promoters [ 50].

A log-odds matrix was constructed from the position weight matrix by using the base 2 logarithm of the ratio of frequencies at each matrix position against a background frequency of 0.25 for each nucleotide.

In addition we show the source network and the directed connectivity of the background frequency oscillations for continuous spikes and waves during slow wave sleep.

The 5′ 1.0 Kbp upstream region was extracted from all D. pulex gene models and used to create a background frequency model for 8 bp length motifs in Daphnia promoter regions.