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Strategies for Multiple Sequence Alignment [PDF]

open access: goldBioTechniques, 2002
We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence ...
Hugh B. Nicholas   +2 more
doaj   +2 more sources

Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning

open access: yesIEEE Open Journal of Engineering in Medicine and Biology, 2021
Goal: Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used method for comparative analysis of biological genomes.
Yong-Joon Song   +4 more
doaj   +1 more source

Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework

open access: yesFrontiers in Genetics, 2021
As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search.
Haipeng Shi   +3 more
doaj   +1 more source

Developments in Algorithms for Sequence Alignment: A Review

open access: yesBiomolecules, 2022
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately.
Jiannan Chao, Furong Tang, Lei Xu
doaj   +1 more source

NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences

open access: yesBMC Bioinformatics, 2021
Background The high variability in envelope regions of some viruses such as HIV allow the virus to establish infection and to escape subsequent immune surveillance. This variability, as well as increasing incorporation of N-linked glycosylation sites, is
Elma H. Akand, John M. Murray
doaj   +1 more source

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment

open access: yesAlgorithms for Molecular Biology, 2023
Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or ...
Chengze Shen   +3 more
doaj   +1 more source

Algorithms for normalized multiple sequence alignments [PDF]

open access: yes, 2021
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the simultaneous alignment of multiple sequences proved to be naturally more intricate.
arxiv   +1 more source

A benchmark study of sequence alignment methods for protein clustering

open access: yesBMC Bioinformatics, 2018
Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment ...
Yingying Wang, Hongyan Wu, Yunpeng Cai
doaj   +1 more source

Explaining human mobility predictions through a pattern matching algorithm

open access: yesEPJ Data Science, 2022
Understanding what impacts the predictability of human movement is a key element for the further improvement of mobility prediction models. Up to this day, such analyses have been conducted using the upper bound of predictability of human mobility ...
Kamil Smolak   +2 more
doaj   +1 more source

GSAlign: an efficient sequence alignment tool for intra-species genomes

open access: yesBMC Genomics, 2020
Background Personal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation.
Hsin-Nan Lin, Wen-Lian Hsu
doaj   +1 more source

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