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Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences .
For a set S of sequences, three sizes matter: the number n of sequences, the size a = |A| of the alphabet, and the length l of the sequences (that could be different for each sequence). In social sciences, n is generally something between a few hundreds and a few thousands, the alphabet size remains limited (most often less than 20), while ...
Alignment-free methods can broadly be classified into five categories: a) methods based on k-mer/word frequency, b) methods based on the length of common substrings, c) methods based on the number of (spaced) word matches, d) methods based on micro-alignments, e) methods based on information theory and f) methods based on graphical representation.
Sequence analysis tasks are often non-trivial to resolve and require the use of relatively complex approaches, many of which are the backbone behind many existing sequence analysis tools. Of the many methods used in practice, the most popular include the following: Dynamic programming; Artificial neural network; Hidden Markov model; Support ...
[3] [14] It also requires an extremely high sequencing depth of around 5 billion paired-end reads per sample to achieve the resolution of data described by Rao et al. [3] [14] [22] Several techniques that have adapted the concept of in situ Hi-C exist, including Sis Hi-C, OCEAN-C and in situ capture Hi-C. [3] Described below are two of the most ...
When data are temporally correlated, straightforward bootstrapping destroys the inherent correlations. This method uses Gaussian process regression (GPR) to fit a probabilistic model from which replicates may then be drawn. GPR is a Bayesian non-linear regression method.
Whereas the methods above describe various sequencing methods, separate related terms are used when a large portion of a genome is sequenced. Several platforms were developed to perform exome sequencing (a subset of all DNA across all chromosomes that encode genes) or whole genome sequencing (sequencing of the all nuclear DNA of a human).
Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...