Accelerated large-scale multiple sequence alignment [PDF]
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of ...
Lloyd Scott, Snell Quinn O
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MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts [PDF]
BMC Bioinformatics, 2011 Background Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif ...
Deng Xin, Cheng Jianlin
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity [PDF]
BMC Bioinformatics, 2004 BackgroundIn a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy
Robert C. Edgar
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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. [PDF]
Brief Bioinform, 2019 This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large ...
Katoh K, Rozewicki J, Yamada KD.
europepmc +2 more sources
MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data [PDF]
BMC Bioinformatics, 2010 Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods.
Kryukov Kirill, Saitou Naruya
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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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Kalign 3: multiple sequence alignment of large data sets. [PDF]
Bioinformatics, 2019 Motivation Kalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. However, current alignment problems involving large numbers of sequences are exceeding Kalign’s original design ...
Lassmann T.
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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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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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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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