FAMSA: Fast and accurate multiple sequence alignment of huge protein families [PDF]
Scientific Reports, 2016 Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment ...
Sebastian Deorowicz +2 more
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Strategies for Multiple Sequence Alignment [PDF]
BioTechniques, 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
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Enhanced Genetic Method for Optimizing Multiple Sequence Alignment [PDF]
Mathematics, 2023 In the realm of bioinformatics, Multiple Sequence Alignment (MSA) is a pivotal technique used to optimize the alignment of multiple biological sequences, guided by specific scoring criteria.
Mohammed K. Ibrahim +3 more
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RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. [PDF]
RNA, 2020 The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments.
Wright ES.
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Progressive multiple sequence alignment with indel evolution [PDF]
BMC Bioinformatics, 2018 Background Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a ...
Massimo Maiolo +3 more
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DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. [PDF]
Bioinformatics, 2020 MOTIVATION The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins ...
Zhang C +4 more
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Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences [PDF]
AlgorithmsThe standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad +2 more
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Multiple sequence alignment with user-defined anchor points [PDF]
Algorithms for Molecular Biology, 2006 Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.
Pöhler Dirk +3 more
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A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains. [PDF]
Sci Rep, 2019 Studies on the structures and functions of individual kinases have been used to understand the biological properties of other kinases that do not yet have experimental structures.
Modi V, Dunbrack RL.
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TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction: Figure 1. [PDF]
Nucleic Acids Res., 2015 This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index.
Jia‐Ming Chang +4 more
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