Results 61 to 70 of about 4,504,319 (408)
Optimization of sequence alignment for simple sequence repeat regions
BMC Research Notes, 2011 Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome.
Ogbonnaya Francis C +2 more
doaj +1 more source
Local Alignment of DNA Sequence Based on Deep Reinforcement Learning
IEEE Open Journal of Engineering in Medicine and Biology, 2021 Goal: Over the decades, there have been improvements in the sequence alignment algorithm, with significant advances in various aspects such as complexity and accuracy. However, human-defined algorithms have an explicit limitation in view of developmental
Yong-Joon Song, Dong-Ho Cho
doaj +1 more source
Fast sequence to graph alignment using the graph wavefront algorithm [PDF]
arXiv, 2022 Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the construction and the analysis of pan-genome graphs. However, existing algorithms incur runtime proportional to the
arxiv
BEAST: Bayesian evolutionary analysis by sampling trees [PDF]
, 2007 Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics ...
Drummond, Alexei J., Rambaut, Andrew
core +3 more sources
Alignment of Biological Sequences with Jalview [PDF]
, 2020 AbstractIn this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview’s core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from
Kira Mourão +15 more
openaire +4 more sources
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
BMC Bioinformatics, 2010 Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám +3 more
doaj +1 more source
Sequence Alignment Using Machine Learning-Based Needleman–Wunsch Algorithm
IEEE Access, 2021 Biological pairwise sequence alignment can be used as a method for arranging two biological sequence characters to identify regions of similarity. This operation has elicited considerable interest due to its significant influence on various critical ...
Amr Ezz El-Din Rashed +3 more
doaj +1 more source
Pairwise heuristic sequence alignment algorithm based on deep reinforcement learning [PDF]
arXiv, 2020 Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the traditional sequence alignment method is considerably complicated in proportion to the sequences' length, and it is ...
arxiv
Alignment of asymmetric-top molecules using multiple-pulse trains [PDF]
Phys. Rev. A 81, 065401 (2010), 2010 We theoretically analyze the effectiveness of multiple-pulse laser alignment methods for asymmetric-top molecules. As an example, we choose SO_2 and investigate the alignment dynamics induced by two different sequences, each consisting of four identical laser pulses. Each sequence differs only in the time delay between the pulses. Equally spaced pulses
arxiv +1 more source
A two-base encoded DNA sequence alignment problem in computational biology [PDF]
, 2009 The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics.
Chang, Jen-Mei +12 more
core