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Reducing storage requirements for biological sequence comparison
Open accessAbstract
MOTIVATION: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seed-and-extend' approach, in which occurrences of short subsequences called 'seeds' are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process. RESULTS: We present a simple and elegant method in which only a small fraction of seeds, called 'minimizers', needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.
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“is a tradeoff between sensitivity and specificity”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [23]
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“The minimizer index data structure was first invented to reduce storage space for biological sequence data [23].”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [23]
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“Since then, minimizers have proven invaluable as a means of providing promising seeds for potential extension during alignment.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [23]
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Cites
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Designing efficient randstrobes for sequence similarity analyses
Karami, M., Mohammadi, A. S., Martin, M., et al. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae187 · Cited by 2
“Strobemers can produce seed matches across substitutions, insertions, and deletions, expanding on ideas from neighboring minimizer pairs (Chin and Khalak 2019, Sahlin and Medvedev 2021) and k -min- mers (Ekim et al. 2021) that link neighboring minimizers (Roberts et al. 2004) into a seed.”
BackgroundFrom PDB files to protein features: a comparative analysis of PDB bind and STCRDAB datasets
Ali, S., Chourasia, P., & Patterson, M. (2024) · Medical & Biological Engineering & Computing · doi:10.1007/s11517-024-03074-3 · Cited by 3
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RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms
Yan, L., Yin, Z., Li, J., Yang, Y., Zhang, T., Zhu, F., Duan, X., Schmidt, B., & Liu, W. (2024) · Lecture notes in computer science · doi:10.1007/978-981-97-5131-0_8 · Cited by 2
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De novo clustering of large long-read transcriptome datasets with isONclust3
Petri, A. J., & Sahlin, K. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf207 · Cited by 2
“In the second step, reads are iterated over in the sorted order and the first read forms a cluster and subsequently all reads are compared to existing clusters, using minimizers (Roberts et al. 2004).”
Integer Programming Framework for Pangenome-Based Genome Inference
Chandra, G., Hossen, M. H., Scholz, S., Dilthey, A., Gibney, D., & Jain, C. (2025) · Lecture notes in computer science · doi:10.1007/978-3-031-90252-9_49 · Cited by 1
Real-time raw signal genomic analysis using fully integrated memristor hardware
He, P., Wang, S., Mao, R., Jiang, M., Siegel, S., Pedretti, G., Ignowski, J., Strachan, J. P., Luo, R., & Li, C. (2025) · Nature Computational Science · doi:10.1038/s43588-025-00867-w · Cited by 2
“To further improve the scalability and efficiency, future work can implement the minimizer technique 14,52 , which selects representative k -mers as input and reference instead of using all k -mers.”
A bucket index correction based method for compression of genomic sequencing data
Wang, R., Bai, Y., Cheng, Q., et al. (2017) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2017.8217727 · Cited by 2
“ORCOM [7] utilizes the concept of “minimizers” [8] to distribute the sequences into disk bins then compress each bin.”
MethodIdentification of Genome Sequences of Polyphosphate-Accumulating Organisms by Machine Learning
Liu, B., Nan, J., Zu, X., et al. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.626221 · Cited by 2
“Minimap2 is based on identifying reads that share many co-linear minimizers (Roberts et al., 2004).”
BackgroundAli, S., & Patterson, M. (2023) · J — Multidisciplinary Scientific Journal · doi:10.3390/j6040038 · Cited by 2
Screening Host Genomic Data for Wolbachia Infections
Valerio, F., Twort, V., & Duplouy, A. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3553-7_16 · Cited by 2
Guguchkin, E., Kasianov, A. S., Беленикин, М. С., Zobkova, G., Kosova, E. V., Makeev, V. J., & Karpulevich, E. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05862-y · Cited by 2
“One of the key features of the minimap2 tool is the use of minimizers [15].”
MethodAn Efficient Parallel Sketch-Based Algorithmic Workflow for Mapping Long Reads
Rahman, T., Bhowmik, O., & Kalyanaraman, A. (2024) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2024.3489478 · Cited by 2
“To improve scalability of mapping, there has been a growing interest in alignment-free approaches [21–25], and in particular sketching—e.g., minimizers [25,26] 5/31 and MinHashing [27].”
BackgroundMethodSpouge, J. L. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac604 · Cited by 2
Zhu, K., Numanagić, I., & Şahinalp, S. C. (2018) · Encyclopedia of Big Data Technologies · doi:10.1007/978-3-319-63962-8_55-1 · Cited by 2
Gerbil: A Fast and Memory-Efficient $k$-mer Counter with GPU-SupportPreprint
Erbert, M., Rechner, S., & Müller‐Hannemann, M. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1607.06618 · Cited by 2
“• Roberts et al. [16]: they propose the lexico-graphic ordering of minimizers with respect to C < A < T < G .”
BackgroundMethods for De-novo Genome AssemblyPreprint
Bayat, A., Gamaarachchi, H., Deshpande, N., Wilkins, M. R., & Parameswaran, S. (2020) · Preprints.org · doi:10.20944/preprints202006.0324.v1 · Cited by 3
“Minimap2 uses Minimizers [40] to reduce the number of k-mers in the dataset to be indexed.”
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Sadasivan, H., Maric, M., Dawson, E., Iyer, V., Israeli, J., & Narayanasamy, S. (2022) · Research Square · doi:10.21203/rs.3.rs-1523696/v1 · Cited by 2
Aligning Distant Sequences to Graphs using Long Seed SketchesPreprint
Joudaki, A., Meterez, A., Mustafa, H., Koerkamp, R. G., Kahles, A., & Rätsch, G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.26.513890 · Cited by 2
Alignment-free Phylogenetic Placement and its Applications
Blanke, M. (2023) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9762 · Cited by 3
Finimizers: Variable-length bounded-frequency minimizers for k -mer setsPreprint
Alanko, J., Biagi, E., & Puglisi, S. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580943 · Cited by 2
Pangenome-based genome inference using integer programmingPreprint
Chandra, G., Hossen, M. H., Scholz, S., Dilthey, A., Gibney, D., & Jain, C. (2025) · Genome Research · doi:10.1101/gr.280567.125 · Cited by 2
The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches
Spouge, J. L., Das, P., Chen, Y., et al. (2024) · Journal of Computational Biology · doi:10.1089/cmb.2024.0508 · Cited by 1
“…are among the oldest submers (Roberts et al., 2004; Schleimer et al., 2003), and they and related techniques have many mature applications such as read mapping (Li, 2018), taxonomy (Wood et al., 2019), and sequence assembly, among others (Roberts et al., 2004; Sommer et al., 2007; Ye et al., 2012).”
A Novel Methodology for a Comprehensive Analysis of Genomic Sequence-to-Graph Alignment Tools
Coggi, M., Donato, G. W. D., & Santambrogio, M. D. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2024.3515469 · Cited by 1
“Its implementation, GraphAligner [40], uses a Seed-And-Extend method with minimizer-based seeding [54], clusters the seeds with superbubbles [56], and finally aligns with a bit-parallel banded DP algorithm.”
xRead: a coverage-guided approach for scalable construction of read overlapping graph
Kong, T., Wang, Y., & Liu, B. (2025) · GigaScience · doi:10.1093/gigascience/giaf007 · Cited by 1
Accelerating k-mer-based sequence filtering
Martayan, I., Vandamme, L., Constantinides, B., et al. (2026) · Peer Community Journal · doi:10.24072/pcjournal.735 · Cited by 1
Fast and flexible minimizer digestion with digest
Zheng, A., Lee, I., Shivakumar, V. S., et al. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf368 · Cited by 1
“Digestion works by selecting certain substrings to be kept according to strategies like minimizers (Schleimer et al. 2003, Roberts et al. 2004) or syn-cmers (Edgar 2021).”
SWBWA: A Highly Efficient NGS Aligner on the New Sunway Architecture
Yan, L., Yin, Z., Chang, Q., et al. (2025) · Lecture notes in computer science · doi:10.1007/978-3-031-99872-0_13 · Cited by 1
SKiM: accurately classifying metagenomic ONT reads in limited memory
Schneggenburger, T., & Żola, J. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf537 · Cited by 1
“One standard way to address this is to sub-sample the k -mers when forming the matrix (e.g. using minimizers (Roberts et al. Figure 1.”
Rice, S. V., Edmonson, M. N., Chen, X., Greenhalgh, R., Rusch, M., Tian, L., Wheeler, D. A., Wang, L., Blackburn, P. R., Cardenas, M., et al. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101238 · Cited by 2
“As noted by Roberts et al., 13 the statistical significance of matching minimizers is increased if h ( q ) is small when q is a rare k -mer and large when q occurs frequently.”
Influentialmm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing
Suzuki, H., Sugawa, M., Sakamoto, Y., et al. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf648 · Cited by 1
“This algorithm, interval hashing, encodes the distances between occurrences of identical k-mers or minimizers (Roberts et al. 2004) into hash values, enabling the distinction of identical k-mers based on their surrounding repeat contexts.”
RapidAVA: Efficient All-vs-All Overlap Detection in HiFi Reads
Cheng, Y., Chen, Z., & Luo, Q. (2025) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm66473.2025.11356060 · Cited by 1
“We identify the first type as the local minimizer in this paper, which is defined as the minimum k-mer within a given sliding window [17].”
Mamede, R., Vila-Cerqueira, P., Carriço, J. A., & Ramirez, M. (2026) · Genome Medicine · doi:10.1186/s13073-026-01625-x · Cited by 1
Building and applying pangenome references to capture genetic diversity
Ashraf, H., Doerr, D., Ebler, J., & Marschall, T. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00987-7 · Cited by 1
Almutairy, M., & Torng, E. K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0179046 · Cited by 1
BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs
Wang, R., Li, J., Bai, Y., Zang, T., & Wang, Y. (2018) · PeerJ · doi:10.7717/peerj.5611 · Cited by 1
“ORCOM (Grabowski, Deorowicz & Roguski, 2015) utilizes the concept of ‘minimizer’ (Roberts et al., 2004) to dispatch similar read sequences into the same disk bin and compresses each bin separately.”
BackgroundMethodA Bloom filter based semi‐index on q‐grams
Grabowski, S., Susik, R., & Raniszewski, M. (2016) · Software Practice and Experience · doi:10.1002/spe.2431 · Cited by 1
“…BFSI-SAM (sampled q -grams), which inserts every s th, s > 1 , sampled q -gram to a BF; note that s D 1 corresponds to the BFSI-STD variant, BFSI-MSAM (minimizer-based sampled q -grams), which is similar to BFSI-SAM, but samples the q -grams in a non-regular way, using the idea of minimizers [22].”
MethodA survey on de novo assembly methods for single‐molecular sequencing
Chen, Y., & Xiao, C. (2020) · Quantitative Biology · doi:10.1007/s40484-020-0214-5 · Cited by 1
“Minimizers [32] are proposed as a replacement of kmers for reducing storage requirements and not reducing the searching sensitivity at the same time.”
BackgroundTang, T., Hutvágner, G., Wang, W., & Li, J. (2022) · Briefings in Functional Genomics · doi:10.1093/bfgp/elac016 · Cited by 1
Ultra-fast and High-quality Mapping of Error-prone Long Reads
Sun, B. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385755 · Cited by 1
“Different from the original minimizer idea [6] adopted in minimap2 , universe minimizer space method extends to global minimality criteria without limitation on a fixed-length sliding window but generates a l -mer space U with size θ l as θ is the size of the alphabet.”
MethodLevallois, V., Andreace, F., Gal, B. L., et al. (2024) · iScience · doi:10.1016/j.isci.2024.111435 · Cited by 1
MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files
Patsakis, M., Provatas, K., Karatzikos, A., Koilakos, C., Mouratidis, I., & Georgakopoulos-Soares, I. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06172-7 · Cited by 1
Expected Density of Random Minimizers
Golan, S., & Shur, A. M. (2025) · Lecture notes in computer science · doi:10.1007/978-3-031-82670-2_25 · Cited by 1
“Minimizers [15, 19] provide a very simple way to sample k -mers for sketching and are also used in more involved sampling schemes such as syncmers [3], strobemers [17], and mod-minimizers [8].”
Parallelizing RNA-Seq Analysis with BioSkel: A FastFlow Based Prototype
Beauvais, V., Tonci, N., Robert, S., & Limet, S. (2025) · International Journal of Parallel Programming · doi:10.1007/s10766-025-00786-3 · Cited by 1
“Another example used in a different field (genomics) is the use of minimizers [17] as representative strings of the genome, which avoid storing and searching repeated sequences [18, 19].”
Accelerating long-read overlap detection for genome assembly with a two-hash table strategy
Eghdami, M., Naghibzadeh, M., & Noori, H. (2025) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2025.108576 · Cited by 1
Singh, N., Khan, J., & Patro, R. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf234 · Cited by 1
“The third, and the fastest method is Chromap (Zhang et al. 2021), which uses a minimizer-based (Roberts et al. 2004) index to map reads by generating candidate anchors from minimizer hits and aligning candidate positions to the reference.”
Text indexing for long patterns using locally consistent anchors
Ayad, L. A. K., Loukides, G., & Pissis, S. P. (2025) · The VLDB Journal · doi:10.1007/s00778-025-00935-7 · Cited by 1
“3 To achieve this, we use minimizers [90, 93], another well-known type of lc-anchors, as anchors to compute A (cid:2) ( S ) (or A h ( S ) ) after carefully setting the sampling parameters.”
InfluentialREINDEER2: Practical Abundance Index at Scale
Hernandez--Courbevoie, Y., Salson, M., Bessière, C., et al. (2025) · Lecture notes in computer science · doi:10.1007/978-3-032-05228-5_14 · Cited by 1
A Simplified Description of Child Tables for Sequence Similarity Search
Frith, M. C., & Shrestha, A. M. S. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2796064 · Cited by 1
“A promising variant of this is “minimizers”, where we only consider hits starting at positions that are “minima” in sliding windows of w consecutive positions [10], [11].”
BackgroundParallel Read Partitioning for Concurrent Assembly of Metagenomic Data
Rengasamy, V., Kandemir, M., Medvedev, P., & Madduri, K. (2018) · IEEE International Conference on High Performance Computing, Data, and Analytics · doi:10.1109/hipc.2018.00044 · Cited by 1
“[25] introduced minimizers for reducing memory requirement for performing seed-and-extend based string search.”
BackgroundEfficient Search over Genomic Short Read Data
Zhang, W., Lin, M., & Ross, K. A. (2020) · International Conference on Scientific and Statistical Database Management · doi:10.1145/3400903.3400907 · Cited by 1
“This work uses lexicographically small minimizers as originally proposed in [38], and hand-picked rules like choosing substrings without AAA at their beginning to avoid”
MethodImprove Spark-based Application Performance Using Minimizer
Wu, J., Deng, L., Wang, L., et al. (2020) · IEEE Data Driven Control and Learning Systems Conference (DDCLS) · doi:10.1109/ddcls49620.2020.9275184 · Cited by 1
HETEROGENEOUS COMPUTING TO ACCELERATE THE SEARCH OF SUPER K-MERS BASED ON MINIMIZERS
Vera-Parra, N. E., Sarmiento, D. A. L., & Rojas-Quintero, C. A. (2020) · International Journal of Computing · doi:10.47839/ijc.19.4.1985 · Cited by 1
“Minimizers were initially proposed as a technique to reduce storage requirements in biological sequence comparison processes [4, 5], through the strategy of reducing the redundancy presented by the “seed-and-extend” technique [6].”
MethodDistributed de novo assembler for large-scale long-read datasets
Goswami, S. C., Lee, K., & Park, S. (2020) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata50022.2020.9377979 · Cited by 1
“Another method of selecting anchor k -mers is by us-ing minimizers [17].”
MethodMultiprocessing Implementation for Building a DNA q-gram Index Hash Table
Mercado, C. C., Fajardo, A. R., Manalili, S. K., et al. (2021) · Lecture notes in electrical engineering · doi:10.1007/978-981-33-4069-5_16 · Cited by 1
Democratizing long-read genome assembly
Kirsche, M., & Schatz, M. C. (2021) · Cell Systems · doi:10.1016/j.cels.2021.09.010 · Cited by 1
Frigate: a fast, in-memory tool for counting and querying k-mers
Brihadiswaran, G., & Jayasena, S. (2021) · International Conference on Bioinformatics and Biomedical Technology (ICBBT) · doi:10.1145/3473258.3473279 · Cited by 1
“The idea of minimizers to efficiently store k -mers was first introduced by Roberts et al. [19] and was adopted into k -mer counting for the first time in MSPKmerCounter.”
MethodPractical universal k -mer sets for minimizer schemesPreprint
DeBlasio, D., Gbosibo, F., Kingsford, C., & Marçais, G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/652925 · Cited by 1
State-of-the-art structural variant calling: What went conceptually wrong and how to fix it?Preprint
Schmidt, M. R., & Kutzner, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.12.426317 · Cited by 1
“In this context, we apply an occurrence filtering that eliminates hash table entries of Minimizers with too many matches on the reference genome or the sequenced genome.”
MethodInfluentialAccelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-DesignPreprint
Cali, D. S. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2111.01916 · Cited by 1
Zhu, K., Numanagić, I., & Şahinalp, S. C. (2019) · Encyclopedia of Big Data Technologies · doi:10.1007/978-3-319-77525-8_55 · Cited by 1
Memory-bound k -mer selection for large and evolutionary diverse reference librariesPreprint
Şapcı, A. O. B., & Mirarab, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.12.580015 · Cited by 1
“Minimization is the standard technique that selects some among adjacent k -mers (Zheng et al., 2023; Roberts et al., 2004) and is adopted by most tools.”
Method<tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings
Rubin, J., van Waaij, J., Kraft, L., Sirén, J., Sackett, P. W., & Renaud, G. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf170 · Cited by 1
“The resulting hash table is called the ( w , k ) -minimizer index [ 23 , 25 ].”
Detecting and correcting errors in genome assemblies
Subramanian, P. (2010) · University Libraries (University of Maryland)
Disk-based genome sequencing data compressionPreprint
Grabowski, S., Deorowicz, S., & Roguski, Ł. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1405.6874
“Still, the major problem with this approach in reads compression concerns the bin criterion: how to detect similar (overlapping) reads, in order to pass them into the same bin? Our solution makes use of the idea of minimizers (Roberts et al., 2004), a late bloomer in bioinformatics, cf.”
BackgroundMethodFull-text and Keyword Indexes for String SearchingPreprint
Cisłak, A. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1508.06610
Improving Sequence Assembly of the Rat Genome Using Reliable Overlaps and Extended Reads
Hayes, W. B., Hunt, B. R., Roberts, M., Yorke, J. A., Zimin, A. V., & Havlak, P. (2005)
Earmark graph approach to de novo genome assembly
Dvorkin, M. V., Kulikov, A. S., & Alekseyev, M. A. (2011) · F1000Research · doi:10.7490/f1000research.1891.1
A bloated FM-index reducing the number of cache misses during the searchPreprint
Grabowski, S., & Cisłak, A. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1512.01996
“[17] and seemingly first overlooked in the bioinformatics (or string matching) community, only to be revived in the last years (e.”
BackgroundTabrizi, M., & Sadat, N. (2015)
Vera-Parra, N. E., Medina-Daza, R. J., & Rojas-Quintero, C. A. (2016) · International Journal of Bioscience Biochemistry and Bioinformatics · doi:10.17706/ijbbb.2016.6.2.59-67
Fast and memory-efficient noisy read overlapping with KD-treesPreprint
Parkhomchuk, D., Bremges, A., & McHardy, A. C. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/166835
“For example, it might be possible to significantly reduce the considered number of k -mers by with a minimizer-like approach (Roberts et al. , 2004).”
Holley, G. (2018) · Publikationen an der Universität Bielefeld (Universität Bielefeld)
Repetitive DNA sequence assembly
Jiang, Y. (2018) · Figshare
High-Performance Computing Frameworks for Large-Scale Genome Assembly
Goswami, S. (2019) · doi:10.31390/gradschool_dissertations.4942
“A more sensitive method of selecting anchor k-mers is by using the Minimizers [52].”
MethodSampling the suffix array with minimizersPreprint
Grabowski, S., & Raniszewski, M. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1406.2348
“The idea of mini-mizers was proposed by Roberts et al. in 2004 [21] and seemingly first overlooked in the bioinformatics (or string matching) community, only to be revived in the last years (cf., e.g., [18,16,3,23]).”
BackgroundDistributed stream-processing framework for graph-based sequence alignment
Gökkaya, A. Ş. (2020) · Bilkent University Institutional Repository (Bilkent University)
Improved Analysis of High-Throughput Sequencing Data Using Small Universal k-Mer Hitting Sets
Orenstein, Y. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1103-6_5
Yu, Y. W. (2021) · arXiv (Cornell University)
Fast-HBR: Fast hash based duplicate read remover
Altayyar, S. (2022) · Bioinformation · doi:10.6026/97320630018036
Current awareness on comparative and functional genomics
(2005) · Comparative and Functional Genomics · doi:10.1002/cfg.422
Ron Shamir, A. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739586121.793585684
Noé, L. (2022) · doi:10.1002/9781394169641.ch3
Taming Large-Scale Genomic Analyses via Sparsified GenomicsPreprint
Alser, M., Eudine, J., & Mutlu, O. (2022) · Research Square · doi:10.21203/rs.3.rs-2277358/v1
Nucleotide String Indexing using Range Matching
Rashelbach, A., Rottenstreich, O., & Silberstein, M. (2023) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3584371.3613024
“…which is known to be one of the primary factors contributing to the total system cost . aligners use a very effective approach called minimizers [26]. state-of-the-art hardware accelerators either use tens of GBs for processing a single reference genome [5, 29], involve special memory In this…”
BackgroundGuguchkin, E., Kasianov, A. S., Беленикин, М. С., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-3953362/v1
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries
Şapcı, A. O. B., & Mirarab, S. (2024) · Lecture notes in computer science · doi:10.1007/978-1-0716-3989-4_26
Song, L., & Langmead, B. (2024) · Lecture notes in computer science · doi:10.1007/978-1-0716-3989-4_22
Methods for Pangenomic Core Detection
Schulz, T., Parmigiani, L., Rempel, A., & Stoye, J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3838-5_4
A fast and simple approach to k -mer decompositionPreprint
Kunzmann, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.26.605312
“This means that 𝑘 -mers with low complexity such as 𝙰𝙰𝙰… would always be the smallest 𝑘 -mer, leading to more spurious than significant 𝑘 -mer matches downstream [5].”
BackgroundMethodInfluentialDNA sequences alignment method using sparse index on pan-genome graph
Gao, J., & Xu, Y. (2024) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720024500197
Accelerating whole-genome alignment in the age of complete genome assembliesPreprint
Chandra, G., Md, V., Misra, S., & Jain, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.25.625328
Construction of edit-distance graphs for large sets of short reads through minimizer-bucketing
Ping, P., & Li, J. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf081
“Although the minimizer strategy was initially proposed to reduce memory consumption and accelerate sequence overlapping detection (Roberts et al. 2004a), it has been shown useful for indexing sequences to facilitate rapid search for matched sequences in read mappers (Ren and Chaisson 2021, Jain et…”
Variable strings for pangenomes
Gabory, E. (2025) · doi:10.5463/thesis.1173
Metadata
- Authors
- Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., & Yorke, J. A.
- Affiliations
- University of Maryland, College Park (US)
- Corresponding author
- Roberts, Michael
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-15
- Volume
- 20
- Issue
- 18
- Pages
- 3363-3369
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2144560237
- Cited by
- 485
- References
- 12
- Citations by year
- 2026: 30 · 2025: 57 · 2024: 65 · 2023: 81 · 2022: 49 · 2021: 49 · 2020: 40 · 2019: 31 · 2018: 26 · 2017: 18 · 2016: 8 · 2015: 10 · 2014: 8 · 2013: 3 · 2012: 3
- FWCI
- 1.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0312360, 0104087, 0114792)
- National Institutes of Health
- National Human Genome Research Institute (1R01HG0294501)
- Topics
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- minimizers, string matching, sequence comparison, storage reduction, nucleic acid sequences, protein sequences, sequence databases
- MeSH terms
- Algorithms, Numerical Analysis, Computer-Assisted, Information Storage and Retrieval, Sequence Alignment, Sequence Analysis, Databases, Genetic
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