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On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences
Springer Science and Business Media LLC - Tập 1 - Trang 1-17 - 2006
Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree. This article introduces a new method of clustering which partitions S into subsets such that the overlap of each pair of sequences within a subset is at least a given percentage c of the...... hiện toàn bộ
Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments
Springer Science and Business Media LLC - Tập 7 - Trang 1-16 - 2012
Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and c...... hiện toàn bộ
Noisy: Identification of problematic columns in multiple sequence alignments
Springer Science and Business Media LLC - Tập 3 - Trang 1-10 - 2008
Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of...... hiện toàn bộ
Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis
Springer Science and Business Media LLC - Tập 11 - Trang 1-10 - 2016
Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a low turnaround time and a high sensitivity. Pyrosequencing suffers however from two main drawbacks including (i) low specificity and (ii) difficult signal interpretation when multiple mutations...... hiện toàn bộ
Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail
Springer Science and Business Media LLC - Tập 2 - Trang 1-17 - 2007
The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For this case, the distribution is only known empirically in the high-probability region, which is biologically less relevant. We provide a method to obtain numerically the biologically relevant r...... hiện toàn bộ
A simple data-adaptive probabilistic variant calling model
Springer Science and Business Media LLC - - 2015
Lossless filter for multiple repeats with bounded edit distance
Springer Science and Business Media LLC - Tập 4 Số 1 - 2009
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
Springer Science and Business Media LLC - Tập 9 - Trang 1-14 - 2014
Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermod...... hiện toàn bộ
Finding the region of pseudo-periodic tandem repeats in biological sequences
Springer Science and Business Media LLC - Tập 1 - Trang 1-8 - 2006
The genomes of many species are dominated by short sequences repeated consecutively. It is estimated that over 10% of the human genome consists of tandemly repeated sequences. Finding repeated regions in long sequences is important in sequence analysis. We develop a software, LocRepeat, that finds regions of pseudo-periodic repeats in a long sequence. We use the definition of Li et al. [1] for the...... hiện toàn bộ
Investigating the complexity of the double distance problems
Springer Science and Business Media LLC - Tập 19 - Trang 1-20 - 2024
Two genomes
$$\mathbb {A}$$
and
$$\mathbb {B}$$
over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Denote by ...... hiện toàn bộ
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