Multiple sequence alignment-based RNA language model and its application to structural inference. [PDF]
Nucleic Acids Res, 2023 Compared to proteins, DNA and RNA are more difficult languages to interpret because 4-letter-coded DNA/RNA sequences have less information content than 20-letter-coded protein sequences. While BERT (Bidirectional Encoder Representations from Transformers)
Zhang Y +13 more
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MAGUS: Multiple sequence Alignment using Graph clUStering. [PDF]
Bioinformatics, 2021 Motivation The estimation of large multiple sequence alignments (MSAs) is a basic bioinformatics challenge. Divide-and-conquer is a useful approach that has been shown to improve the scalability and accuracy of MSA estimation in established methods such ...
Smirnov V, Warnow T.
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Scalable long read self-correction and assembly polishing with multiple sequence alignment. [PDF]
Sci Rep, 2021 Third-generation sequencing technologies allow to sequence long reads of tens of kbp, that are expected to solve various problems. However, they display high error rates, currently capped around 10%.
Morisse P +4 more
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ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. [PDF]
PLoS Biol, 2020 Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference.
Steenwyk JL +4 more
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Recursive MAGUS: Scalable and accurate multiple sequence alignment. [PDF]
PLoS Computational Biology, 2021 Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence data, as few methods can handle large datasets while maintaining alignment accuracy.
Vladimir Smirnov
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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.
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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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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability [PDF]
Molecular biology and evolution, 2013 We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained ...
Kazutaka Katoh, Daron M. Standley
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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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Advances in post-processing methods for multiple sequence alignment [PDF]
Frontiers in GeneticsThe reliability of multiple sequence alignment (MSA) results directly determines the credibility of the conclusions drawn from biological research. However, MSA is inherently an NP-hard problem, making it theoretically impossible to guarantee a globally ...
Yixiao Zhai +3 more
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