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Sequence Alignment in Molecular Biology
Journal of Computational Biology, 1998 Molecular biology is becoming a computationally intense realm of contemporary science and faces some of the current grand scientific challenges. In its context, tools that identify, store, compare and analyze effectively large and growing numbers of bio ...
APOSTOLICO, ALBERTO, R. GIANCARLO
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Integrating sequence and structural biology with DAS [PDF]
BMC Bioinformatics, 2007 Background The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.
Finn Robert D +5 more
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Strainberry: automated strain separation in low-complexity metagenomes using long reads
Nature Communications, 2021 Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and ...
Riccardo Vicedomini +3 more
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Legume Biology: Sequence to Seeds [PDF]
Plant Physiology, 2007 Research on legumes is driven, to a large extent, by their importance as food crops worldwide. Some 25% of the world's major crop production is derived from legumes, and more than one-third of humanity's nutritional nitrogen requirement comes from legumes.
Mark R, O'Brian, Carroll P, Vance
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decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Microbiome, 2023 Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources.
Camila Duitama González +5 more
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Mapping-friendly sequence reductions: Going beyond homopolymer compression
iScience, 2022 Summary: Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present in ...
Luc Blassel, Paul Medvedev, Rayan Chikhi
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Connecting Sequence and Biology in the Laboratory Mouse [PDF]
Genome Research, 2003 The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research.
Richard M, Baldarelli +26 more
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SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction [PDF]
PeerJ, 2023 Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism.
Wu Yan +5 more
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HostPhinder: A Phage Host Prediction Tool
Viruses, 2016 The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput ...
Julia Villarroel +6 more
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RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
iScience, 2021 Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using
Nitesh Kumar Sharma +5 more
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