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   Articles with "sequence alignments" as a keyword



Learning genotype–phenotype associations from gaps in multi-species sequence alignments

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recommendations! Published in 2024 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbaf022

Abstract: Abstract Understanding the genetic basis of phenotypic variation is fundamental to biology. Here we introduce GAP, a novel machine learning framework for predicting binary phenotypes from gaps in multi-species sequence alignments. GAP employs a neural… read more here.

Keywords: genotype phenotype; species sequence; sequence alignments; gaps multi ... See more keywords

Highly significant improvement of protein sequence alignments with AlphaFold2

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recommendations! Published in 2022 at "Bioinformatics"

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

CREMSA: compressed indexing of (ultra) large multiple sequence alignments

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recommendations! Published in 2025 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btaf211

Abstract: Abstract Motivation Recent viral outbreaks motivate the systematic collection of pathogenic genomes in order to accelerate their study and monitor the apparition/spread of variants. Due to their limited length and temporal proximity of their sequencing,… read more here.

Keywords: cremsa compressed; multiple sequence; sequence alignments; sequence ... See more keywords

Ultrafast and ultralarge multiple sequence alignments using TWILIGHT

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recommendations! Published in 2025 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btaf212

Abstract: Abstract Motivation Multiple sequence alignment (MSA) is a fundamental operation in bioinformatics, yet existing MSA tools are struggling to keep up with the speed and volume of incoming data. This is because the runtimes and… read more here.

Keywords: memory; ultralarge multiple; multiple sequence; sequence alignments ... See more keywords

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.

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recommendations! 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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recommendations! 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

Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor

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recommendations! Published in 2020 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"

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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recommendations! 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