For comparing the matrices with strictly positive values, e.g., counts of frequencies, this effect may be less important, but a log-odds PWM can contain negative elements with rather high absolute values, which would substantially bias the comparison.
Key steps in sequence signature methods include the counting of frequencies of all k-tuples to compose the sequence signature vector for each sample, calculating the dissimilarity measure between samples based on their sequence signature vectors, and analyzing relationships between multiple samples based on dissimilarities of all sample pairs.
The independence between individual codon frequencies is quite high since there are 61 codons (and the results are identical if one uses total codon counts instead of frequencies).
Codon equilibrium frequencies can be estimated from data using either simple proportions in the full data set (the CT model with 60 parameters), assuming equal frequencies (Fequal model), multiplying overall counts of nucleotide frequencies (F1 × 4 model, 3 parameters) or counts of nucleotide frequencies for each codon position (F3 × 4 model, 9 parameters).
With a set of observed counts of allele frequencies in hand we aim to find the maximum-likelihood estimate of the site frequency spectrum, <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0005152.e003.PNG" class= inline-graphic"/>.
For the BFC modulated signal in the DFC family, we can recognize it by counting the number of frequencies in the IFL curve.
Topic specific words can be identified by removing words which appear exceeding a threshold measure defined based on ratio of frequency count of documents in which this word appears and frequency count of documents describing the topic of interest [83].
It goes beyond the manifest (or visible) content analysis process of counting frequency of appearance of different words within responses [ 57], to examining language and its meaning.
We have implemented a scoring system, but rather than using counts of domain frequency across all genomes as in previous scoring methods the CODA score uses domain counts within individual genomes.
Errors in the supplied annotation of a set of cDNA clones that were sequenced bidirectionally were identified and corrected to generate accurate counts of EST frequency.
The counts of shivering frequency were significantly decreased (50%) throughout the testing period in patients treated with active core rewarming when compared with those of the controls.
