Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1036-7_7
Abstract: The estimation of very large multiple sequence alignments is a challenging problem that requires special techniques in order to achieve high accuracy. Here we describe two software packages-PASTA and UPP-for constructing alignments on large and… read more here.
Keywords: sequence alignment; multiple sequence; alignment large; pasta upp ... See more keywords
PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.1c01360
Abstract: Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, current molecular design… read more here.
Keywords: visualization; peptide sequence; sequence alignment; pepsea ... See more keywords
A survey on the algorithm and development of multiple sequence alignment
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac069
Abstract: Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as… read more here.
Keywords: sequence alignment; msa; multiple sequence; alignment ... See more keywords
Ggmsa: a Visual Exploration Tool for Multiple Sequence Alignment and Associated Data
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac222
Abstract: The identification of the conserved and variable regions in the multiple sequence alignment (MSA) is critical to accelerating the process of understanding the function of genes. MSA visualizations allow us to transform sequence features into… read more here.
Keywords: associated data; sequence alignment; sequence; multiple sequence ... See more keywords
WMSA 2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad190
Abstract: Multiple sequence alignment is widely used for sequence analysis, such as identifying important sites and phylogenetic analysis. Traditional methods, such as progressive alignment, are time-consuming. To address this issue, we introduce StarTree, a novel method… read more here.
Keywords: time; win win; sequence alignment; sequence ... See more keywords
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx643
Abstract: Abstract Motivation Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have… read more here.
Keywords: hidden states; beyond similarity; similarity assessment; sequence alignment ... See more keywords
Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad400
Abstract: The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these… read more here.
Keywords: sequence alignment; immune repertoires; multiple sequence; alignment ... See more keywords
Measuring Phylogenetic Information of Incomplete Sequence Data.
Sign Up to like & getrecommendations! Published in 2021 at "Systematic biology"
DOI: 10.1093/sysbio/syab073
Abstract: Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of… read more here.
Keywords: information; model misspecification; measuring phylogenetic; sequence alignment ... See more keywords
Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures
Sign Up to like & getrecommendations! Published in 2020 at "IEEE Transactions on Computers"
DOI: 10.1109/tc.2020.3041402
Abstract: Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As… read more here.
Keywords: performance energy; energy savings; energy; sequence alignment ... See more keywords
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem.
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2022.3191848
Abstract: MAGUS is a recent multiple sequence alignment method that provides excellent accuracy on large challenging datasets. MAGUS uses divide-and-conquer: it divides the sequences into disjoint sets, computes alignments on the disjoint sets, and then merges… read more here.
Keywords: problem; maximum weight; sequence alignment; multiple sequence ... See more keywords
Identifying Tourist Spatial and Temporal Patterns Using GPS and Sequence Alignment Method
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Travel Research"
DOI: 10.1177/00472875221127685
Abstract: This study identified the spatial and temporal patterns of national park visitors by combining global positioning system (GPS) technologies and surveys using the sequence alignment method (SAM) based on the concept of space–time path of… read more here.
Keywords: sequence alignment; geography; temporal patterns; alignment method ... See more keywords