Related papers: Multiple Sequence Alignment System for Pyrosequenc…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
It has been shown that a class of probabilistic domain models cannot be learned correctly by several existing algorithms which employ a single-link look ahead search. When a multi-link look ahead search is used, the computational complexity…
Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core…
The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Modern neural networks have greatly improved performance across speech recognition benchmarks. However, gains are often driven by frequent words with limited semantic weight, which can obscure meaningful differences in word error rate, the…
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
In recent years, aligning a sequence to a pangenome has become a central problem in genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple…
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the…