Reducing storage requirements for biological sequence comparison

Roberts, Michael, Hayes, Wayne, Hunt, Brian R., Mount, Stephen M., Yorke, James A.·2004·Bioinformatics
DOI 10.1093/bioinformatics/bth408

Cited by (490)

Items 101–200 of 490

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  14. Spectral Jaccard Similarity: A New Approach to Estimating Pairwise Sequence Alignments
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  22. Sequence-specific minimizers via polar sets
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  23. Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet
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  28. Locality-preserving minimal perfect hashing of k -mers
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  29. Benchmarking machine learning robustness in Covid-19 genome sequence classification
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  35. Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
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  36. High-resolution metagenome assembly for modern long reads with myloasm
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  39. De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm
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  42. Matchtigs: minimum plain text representation of k-mer sets
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  43. A performant bridge between fixed-size and variable-size seeding
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  44. On weighted k-mer dictionaries
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  46. GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
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  47. Compact and evenly distributed k-mer binning for genomic sequences
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  48. KrakenOnMem
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  49. When less is more: sketching with minimizers in genomics
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  51. deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph
    Hongzhe Guo, Yilei Fu, Yan Ping Gao · 2019 · IEEE Transactions on Computational Biology and Bioinformatics
  52. Compact representation of k-mer de Bruijn graphs for genome read assembly
    Einar Andreas Rødland · 2013 · BMC Bioinformatics
  53. Locally Consistent Parsing for Text Indexing in Small Space
    Or Birenzwige, Shay Golan, Ely Porat · 2019 · Society for Industrial and Applied Mathematics eBooks
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  55. Exploring the Potential of GANs in Biological Sequence Analysis
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  56. Efficient mapping of accurate long reads in minimizer space with mapquik
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  57. Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design
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  58. Scalable pairwise whole-genome homology mapping of long genomes with BubbZ
    Minkin, Ilia, Medvedev, Paul · 2020 · iScience
  59. Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer
    Minh Hoang, Hongyu Zheng, Carl Kingsford · 2022 · Journal of Computational Biology
  60. Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining
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  61. De novo Nanopore read quality improvement using deep learning
    Nathan LaPierre, Rob S Egan, Wei Wang, Zhong Wang · 2019 · BMC Bioinformatics
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    Marius Erbert, Steffen Rechner, Matthias Müller‐Hannemann · 2016 · Lecture notes in computer science
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    Yuansheng Liu, Jinyan Li · 2021 · PLoS Computational Biology
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    Miklós Csürös, Bin Ma · 2005 · Lecture notes in computer science
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  68. IMOS: improved Meta-aligner and Minimap2 On Spark
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  69. Dynamic Alignment-Free and Reference-Free Read Compression
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  71. A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
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  72. Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers
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  73. Locityper enables targeted genotyping of complex polymorphic genes
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