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 401–490 of 490

  1. TetRex: a novel algorithm for index-accelerated search of highly conserved motifs
    Remy M Schwab, Simon Gene Gottlieb, Knut Reinert · 2025 · NAR Genomics and Bioinformatics
  2. Kaminari: a resource-frugal index for approximate colored k -mer queries
    Victor Levallois, Yoshihiro Shibuya, Bertrand Le Gal · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  3. VirB: A Virus Hierarchical Classification Method Based on ModernBERT
    Haizhen Huang, Haodi Feng, Daming Zhu · 2025 · Lecture notes in computer science
  4. Quality control of single-cell ATAC-seq data without peak calling using Chromap
    Omar Y. Ahmed, Haowen Zhang, Ben Langmead · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Panaln: indexing pangenome for read alignment
    Lilu Guo, Zongtao He, Hongwei Huo · 2025 · Bioinformatics
  6. Edit Distance Embedding with Genomic Large Language Model
    Xiang Li, Ke Chen, Yi-Jia Zhang, Mingfu Shao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Seqwin: ultrafast identification of signature sequences in microbial genomes
    Michael Wang, Bryce L. Kille, Michael Nute · 2026 · Bioinformatics
  8. System Level Acceleration of Banded Smith Waterman on FPGA
    Christian Lanius, Ibrahim Burak Yorulmaz, Tobias Gemmeke · 2025 · IEEE Nordic Circuits and Systems Conference (NorCAS)
  9. opjMap: A Sensitive Mapper for Repetitive Structural Variations in Long Noisy Reads Based on Orthogonal Projection
    Xing-Guo Fan, Xiaodan Zhang, Cheng-Song Hu, Jie-Jie Zeng, Shu-Rui Li, Ze‐Gang Wei · 2025 · Research Square
  10. Haplotype-resolved diploid genome inference on pangenome graphs
    Ghanshyam Chandra, William T. Doan, Daniel Gibney · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  11. MELO-ED: learning locality-sensitive multi-embeddings for edit distance
    Xin Yuan, Ke Chen, Ajmain Yasar Ahmed, Mingfu Shao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Density-reducing Jaccard estimators for sketch-based long read applications
    Tazin Rahman, Ananth Kalyanaraman · 2025 · BMC Bioinformatics
  13. KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery
    Molly Borowiak, Yun William Yu · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Additional file 1 of Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
    Colquhoun, Rachel M., Michael B. Hall, Leandro Lima, Leah Wendy Roberts, Kerri M. Malone, Hunt, Martin, Brice Letcher, Jane Hawkey, George, Sophie, Louise J. Pankhurst et al. · 2021 · Figshare
  15. Additional file 1 of Technology dictates algorithms: recent developments in read alignment
    Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Taraszka, Kodi, Huwenbo Shi, Pelin Icer Baykal, Yang, Harry Taegyun, Victor Xue, Knyazev, Sergey, Singer, Benjamin D. et al. · 2021 · Figshare
  16. Additional file 4 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  17. Additional file 1 of Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
    Egor Guguchkin, Artem S. Kasianov, М. С. Беленикин · 2024 · Figshare
  18. Additional file 3 of A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
    Du, Ze-Zhen, He, Jia-Bao, Jiao, Wen-Biao · 2024 · Figshare
  19. Additional file 2 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  20. Additional file 6 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  21. Additional file 12 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  22. Additional file 1 of A survey of mapping algorithms in the long-reads era
    Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet · 2024 · Figshare
  23. Additional file 3 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  24. Additional file 1 of Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification
    Li Song, Ben Langmead · 2024 · Figshare
  25. Additional file 1 of smsMap: mapping single molecule sequencing reads by locating the alignment starting positions
    Wei, Ze-Gang, Zhang, Shao-Wu, Liu, Fei · 2020 · Figshare
  26. Additional file 1 of A performant bridge between fixed-size and variable-size seeding
    Arne Kutzner, Kim, Pok-Son, Schmidt, Markus · 2020 · Figshare
  27. Additional file 8 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  28. Additional file 10 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  29. Additional file 1 of Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method
    Yiqing Yan, Nimisha Chaturvedi, Raja Appuswamy · 2021 · Figshare
  30. Additional file 1 of Sketching and sampling approaches for fast and accurate long read classification
    Arun Das, Schatz, Michael C. · 2022 · Figshare
  31. Additional file 14 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  32. Additional file 7 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  33. Additional file 1 of Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Patro, Rob · 2022 · Figshare
  34. Additional file 2 of SPUMONI 2: improved classification using a pangenome index of minimizer digests
    Ahmed, Omar Y., Massimiliano Rossi, Travis Gagie, Boucher, Christina, Ben Langmead · 2023 · Figshare
  35. Additional file 6 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  36. Additional file 2 of A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
    Du, Ze-Zhen, He, Jia-Bao, Jiao, Wen-Biao · 2024 · Figshare
  37. Additional file 2 of A survey of mapping algorithms in the long-reads era
    Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet · 2024 · Figshare
  38. Additional file 5 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  39. Additional file 2 of Technology dictates algorithms: recent developments in read alignment
    Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Yang, Harry Taegyun, Victor Xue, Knyazev, Sergey, Singer, Benjamin D. et al. · 2021 · Figshare
  40. Additional file 2 of Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification
    Li Song, Ben Langmead · 2024 · Figshare
  41. Additional file 1 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  42. Additional file 9 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  43. Additional file 2 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  44. Additional file 2 of Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Patro, Rob · 2022 · Figshare
  45. Additional file 1 of Multiple genome alignment in the telomere-to-telomere assembly era
    Kille, Bryce, Advait Balaji, Fritz Joachim Sedlazeck, Michael Nute, Todd J. Treangen · 2022 · Figshare
  46. Additional file 4 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  47. Additional file 1 of A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
    Du, Ze-Zhen, He, Jia-Bao, Jiao, Wen-Biao · 2024 · Figshare
  48. Additional file 5 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  49. Additional file 13 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  50. Additional file 1 of LongStitch: high-quality genome assembly correction and scaffolding using long reads
    Coombe, Lauren, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolić, Warren, René L., Birol, Inanc · 2021 · Figshare
  51. Additional file 1 of Strobealign: flexible seed size enables ultra-fast and accurate read alignment
    Kristoffer Sahlin · 2024 · Figshare
  52. Additional file 3 of Matchtigs: minimum plain text representation of k-mer sets
    Sebastian Schmidt, Khan, Shahbaz, Jarno Alanko · 2024 · Figshare
  53. Additional file 1 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  54. Additional file 2 of Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
    Colquhoun, Rachel M., Michael B. Hall, Leandro Lima, Leah Wendy Roberts, Kerri M. Malone, Hunt, Martin, Brice Letcher, Jane Hawkey, George, Sophie, Louise J. Pankhurst et al. · 2021 · Figshare
  55. Additional file 15 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  56. Additional file 11 of MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Schmidt, Markus, Arne Kutzner · 2023 · Figshare
  57. Additional file 1 of Comparative analysis of metagenomic classifiers for long-read sequencing datasets
    Josip Marić, Krešimir Križanović, Sylvain Riondet, Niranjan Nagarajan, Mile Šikić · 2024 · Figshare
  58. Minimizers in Semi-dynamic Strings
    Wiktor Zuba, Oded Lachish, Solon P. Pissis · 2025 · Lecture notes in computer science
  59. Generating Minimum-Density Minimizers
    Arseny M. Shur, Ido Tziony, Yaron Orenstein · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  60. Minimizer Sketches of Lyndon-Fingerprints: A Novel Approach to Compute Overlaps Among Long Reads
    Omar Masri, Yuri Pirola, Cristina Borghi, Paola Bonizzoni, Raffaella Rizzi · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  61. Concisemizer: An Asymmetric Redundancy-Removal Algorithm for Efficient Seed Sampling in Large-Scale Sequence Alignment
    Hao Gao, Yangyang Sun, Xiaoquan Su · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  62. A general and extensible algorithmic framework to biological sequence alignment across scales and applications
    Hao Xuan, Hongyang Sun, Xiangtao Liu, Hanyuan Zhang, Jun Zhang, Cuncong Zhong · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  63. k ache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k -mer operations
    Jamshed Khan, Rob Patro, Prashant Pandey · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers
    Jaebeom Kim, Martin Steinegger · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  65. From reads to transcripts : de novo methods for the analysis of transcriptome second and third generation sequencing
    Camille Marchet · 2018 · theses.fr (ABES)
  66. Nouvelles approches pour l'exploitation des données de séquences génomique haut débit
    Antoine Limasset · 2017
  67. Métagénomique comparative de novo à grande échelle
    Gaëtan Benoit · 2017
  68. Minimizing the minimizers via alphabet reordering
    Hilde Verbeek, Lorraine A. K. Ayad, Grigorios Loukides · 2026 · Theoretical Computer Science
  69. Identification of key players in the gut microbiota based on a unified reference for a standardized quantitative metagenomics and metabolic analysis framework
    Marianne Borderes · 2021 · theses.fr (ABES)
  70. Scalable and accurate algorithms for computational genomics and dna-based digital storage
    Yiqing Yan · 2023
  71. Sketching data structures for alignment-free analysis of genomic sequences
    Yoshihiro Shibuya · 2022
  72. From sequences to knowledge, improving and learning from sequence alignments
    Luc Blassel · 2022 · theses.fr (ABES)
  73. Dynamic Pan-genome graphs
    Khodor Hannoush · 2024
  74. Interactions between human papillomaviruses and their host in 3D models of skin epithelia : importance of keratinocyte/fibroblast communications
    Marta Laganà · 2023 · theses.fr (ABES)
  75. Kaminari: a frugal colored index for approximate k -mer queries
    Victor Levallois, Yoshihiro Shibuya, Bertrand Le Gal · 2026 · Bioinformatics Advances
  76. Hash functions in nucleotide sequence analysis
    Ke Chen, Xiang Li, Qian Shi · 2026 · Genome Research
  77. Scalable machine learning improves resistance prediction and identifies novel determinants in Mycobacterium tuberculosis
    Mohammadali Serajian, Mahsa Lotfollahi, Oded Green · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Memory-safe high-performance sequence mapping with rammap
    Jeremy R Wang, Heng Li · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  79. LAMP: An Adaptive Near-Memory Processing System for High-Performance Long-Read Mapping
    Jo-Ling Huang, Liang-Chi Chen, Chien-Chung Ho · 2026 · Design, Automation, and Test in Europe
  80. MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host
    Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar et al. · 2026 · BMC Bioinformatics
  81. A foundational quantum framework for multi-pattern string matching in k-mer detection
    Christos Papalitsas, I. Mouratidis, Michail Patsakis, Evangelos Stogiannos, I. Georgakopoulos-Soares, G. Koulouras · 2026 · Frontiers in Bioinformatics
  82. Optimizing Long-Read Sequence Alignment on a CPU-DSPs Heterogeneous Processor
    Xinjie An, Yi Guo, Yi Guo · 2026 · IEEE Transactions on Computers
  83. High-Quality Large-Scale Viral Genome Multiple Sequence Alignment with Updated HAlign4
    Pinglu Zhang, Qinzhong Tian, Yixiao Zhai · 2026 · Lecture notes in computer science
  84. Lembas: Cost-Efficient Genome Alignment with External Memory and FPGA Acceleration
    Seongyoung Kang, Se-Min Lim, Sang-Woo Jun · 2026 · Proceedings - International Symposium on Computer Architecture/Proceedings
  85. Efficient Genome-by-k-mer Matrix Construction for Population-Scale Health Analytics
    Mohammadali Serajian, Mahsa Lotfollahi, Oded Green · 2026 · IEEE International Conference on Healthcare Informatics (ICHI)
  86. Coverage-Aware Windowed mdBG Assembly
    Wei‐Yu Chen, Yong He, Bin Zhu, Zhenhe Cui · 2026 · International Symposium on Bioinformatics and Computational Biology (BCB)
  87. Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma
    Luuk A. Broeils, Jill Pilet, Maria K. Koshkina, Jing Li, Sandrine Grossetête, Emma G. A. Westerink, Orson Jay, Lotta Smit, Ting Luo, Erkan Narmanli et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Filtr: Compiling Bioinformatics Recurrences
    Bala Vinaithirthan, Shiv Sundram, Sneha D. Goenka, Fredrik Kjolstad · 2026 · Proceedings of the ACM on Programming Languages
  89. Minimizer Density Revisited: Models and Multiminimizers
    Florian Ingels, Lucas Robidou, Igor Martayan · 2026 · Journal of Computational Biology
  90. A Run-Length-Compressed Skiplist Data Structure for Dynamic GBWTs Supports Time- and Space-Efficient Pangenome Operations over Syncmers
    Richard Michael Durbin · 2026 · Journal of Computational Biology