Highly significant improvement of protein sequence alignments with AlphaFold2
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DOI: 10.1093/bioinformatics/btac625
Abstract: Abstract Motivation Protein sequence alignments are essential to structural, evolutionary and functional analysis, but their accuracy is often limited by sequence similarity unless molecular structures are available. Protein structures predicted at experimental grade accuracy, as… read more here.
Keywords: sequence alignments; highly significant; sequence; protein sequence ... See more keywords
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.
Sign Up to like & getrecommendations! Published in 2022 at "Database : the journal of biological databases and curation"
DOI: 10.1093/database/baac025
Abstract: Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment… read more here.
Keywords: pass2 database; sequence alignments; sequence; structure ... See more keywords
Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
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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
Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor
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DOI: 10.1109/tcbb.2018.2884701
Abstract: FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in… read more here.
Keywords: intel; accelerating sequence; sequence alignments; memory ... See more keywords
CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments
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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