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
Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments
Sign Up to like & getrecommendations! Published in 2017 at "Amino Acids"
DOI: 10.1007/s00726-017-2512-4
Abstract: Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To… read more here.
Keywords: classification protein; classification; multiple sequence; protein coupled ... See more keywords
Multiple Sequence Variants in STAC3 Affect Interactions with CaV1.1 and Excitation-Contraction Coupling.
Sign Up to like & getrecommendations! Published in 2020 at "Structure"
DOI: 10.1016/j.str.2020.05.005
Abstract: STAC3 is a soluble protein essential for skeletal muscle excitation-contraction (EC) coupling. Through its tandem SH3 domains, it interacts with the cytosolic II-III loop of the skeletal muscle voltage-gated calcium channel. STAC3 is the target… read more here.
Keywords: contraction coupling; multiple sequence; sh3 domains; sequence variants ... 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
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
Accurate inference of tree topologies from multiple sequence alignments using deep learning.
Sign Up to like & getrecommendations! Published in 2019 at "Systematic biology"
DOI: 10.1093/sysbio/syz060
Abstract: Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies… read more here.
Keywords: topologies multiple; multiple sequence; deep learning; topology ... See more keywords
Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
Sign Up to like & getrecommendations! Published in 2022 at "PLOS ONE"
DOI: 10.1101/2022.12.14.520492
Abstract: The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the… read more here.
Keywords: sequence alignments; genome mappings; multiple sequence; protein genome ... 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
CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0265360
Abstract: Background High-throughput experimental technologies are generating tremendous amounts of genomic data, offering valuable resources to answer important questions and extract biological insights. Storing this sheer amount of genomic data has become a major concern in… read more here.
Keywords: sequence alignments; multiple sequence; compression; biomolecular sequences ... See more keywords
A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment
Sign Up to like & getrecommendations! Published in 2020 at "Frontiers in Immunology"
DOI: 10.3389/fimmu.2020.585731
Abstract: Human chromosome 19q13.4 contains genes encoding killer-cell immunoglobulin-like receptors (KIR). Reported haplotype lengths range from 67 to 269 kb and contain 4 to 18 genes. The region has certain properties such as single nucleotide variation,… read more here.
Keywords: kir; alignment; multiple sequence; kir haplotype ... See more keywords