Previous algorithms have shown that the constrained longest common subsequence problem is a special case of the constrained pairwise sequence alignment problem, and that both of them can be solved in O(rnm) time, where r, n, and m represent the lengths of C, S1, and S2, respectively. In...
Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods...
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generati...
First, alignment-producing programs assume that homologous sequences comprise a series of linearly arranged and more or less conserved sequence stretches. However, this assumption, which is termed collinearity, is very often violated in the real world. A good example is viral genomes, which exhibit ...
High-throughput sequence alignment using Graphics Processing Units p pBackground/p pThe recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume o... T Cole,MC Schatz,AL Delcher,... - 《Bmc Bioinformatics》 被引量: 514...
Targeted DNA can be generated in several different ways: PCR through amplicon sequencing, microdroplet PCR with RainStorm (RainDance Technologies, Lexington, MA, USA) or through sequence capture (NimbleGen, Roche; SureSelect, Agilent Technologies). mRNA can be used in a deep-serial analysis of ...
The aim of this paper is to develop... XC Cai,Y Saad - 《Numerical Linear Algebra with Applications》 被引量: 142发表: 1994年 Reduced space sequence alignment. they can be used in the forward-backward (Baum-Welch) training of linear hidden Markov models, and they avoid data-dependent re...
Sequence data software and pipelines have also been developed to improve the efficiency and versatility of GBS for SNP discovery and mapping10,12,13. For example, UNEAK (Universal Network Enabled Analysis Kit) is a network-based SNP calling pipeline for species without a reference genome, such ...
Multiple sequence alignment: Algorithms and applications Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a centra... O Gotoh - 《Advances in Biophysics》 被引量: 221发表: 1999年 Hybrid intelligent algo...
Archive files in the SRA format (.sra) are converted into the FASTQ or SAM/BAM formats for input to downstream analysis using programs (Table 3) to undertake the second tier analysis of sequence alignment (spliced and genomic), assembly, and variant detection. The requirement for sequence ...