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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...dataWe then tested all methods on reconstructing repeat units for satellite DNA in human Chromosome 5 (Paar et al. 2007). This known satellite DNA consists of 13 units (i.e., 13 monomers), each of which is ∼171 bp in size. To construct the input sequence for methods to predict, we concatenated the 13...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
....The following example highlights the limitations of k-mers, defined as substrings with length k, as candidates for seeding:Example 1(limitations of k-mer seeds). We have a reference sequence, denoted as S, that is uniformly drawn from the set of DNA nucleotides {A, C, G, T}. We create a query sequence q...
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Method: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
- Mădălina Giurgiu,
- Nadine Wittstruck,
- Elias Rodriguez-Fos,
- Rocío Chamorro González,
- Lotte Brückner,
- Annabell Krienelke-Szymansky,
- Konstantin Helmsauer,
- Anne Hartebrodt,
- Philipp Euskirchen,
- Richard P. Koche,
- Kerstin Haase,
- Knut Reinert,
- and Anton G. Henssen
Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
....g., repeats), which pose a challenge to mapping and de novo assembly-based methods. On the other hand, one tumor can contain different ecDNA elements (Hung et al. 2022; Chamorro González et al. 2023), which can originate from either different or shared genomic locations (Verhaak et al. 2019). The latter...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...is the current gold standard for estimating repeat length, but this method is very challenging to set up; requiring a significant amount of input DNA (generally 10 μg) and suffering from imprecise size estimates due to somatic heterogeneity (Buchman et al. 2013; Akimoto et al. 2014). AsWGS is widely adopted...
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Methods: De Novo Repeat Classification and Fragment Assembly
- Paul A. Pevzner,
- Haixu Tang,
- and Glenn Tesler
Genome Res. September 2004 14: 1786-1796; doi:10.1101/gr.2395204
...Department of Mathematics, University of California, San Diego,La Jolla, California 92093, USA Abstract Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose...
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Methods: A novel method for multiple alignment of sequences with repeated and shuffled elements
- Benjamin Raphael,
- Degui Zhi,
- Haixu Tang,
- and Pavel Pevzner
Genome Res. November 2004 14: 2336-2346; doi:10.1101/gr.2657504
...A novel method for multiple alignment of sequences with repeated and shuffled elements Benjamin Raphael 1 , Degui Zhi , Haixu Tang , and Pavel Pevzner Department of Computer Science and Engineering, University of California, San Diego, La...
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LETTER: Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes
- Peter E. Warburton,
- Joti Giordano,
- Fanny Cheung,
- Yefgeniy Gelfand,
- and Gary Benson
Genome Res. October 2004 14: 1861-1869; doi:10.1101/gr.2542904
.... IRs were confirmed by visual analysis of the mirror symmetrical pattern of the RepeatMasker track, and by BLAT searches with DNA sequences from one arm, which always identified the other arm. Each IR is named by the chromosome on which it is found and the approximate genomic coordinates (in megabase...
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LETTERS: Structural Organization of the WD repeat protein-encoding gene HIRA in the DiGeorge syndrome critical region of human chromosome 22.
- S Lorain,
- S Demczuk,
- V Lamour,
- S Toth,
- A Aurias,
- B A Roe,
- and M Lipinski
Genome Res. January 1996 6: 43-50; doi:10.1101/gr.6.1.43
...of the HIR proteins. Individual repeats were found to be encoded from one, two, or three exons of the HIRA gene. End sequences have been obtained for all 24 introns, opening the way to PCR amplification of the entire coding sequence starting from genomic DNA. Point mutations can also be sought in 16...
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METHODS: Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization
- Peter K. Rogan,
- Patricia M. Cazcarro,
- and Joan H.M. Knoll
Genome Res. June 1, 2001 11: 1086-1094; doi:10.1101/gr.171701
.... ( 2000 ) The DNA sequence of human chromosome 21. Nature 405 : 311 – 319 . ↵ Ji Y. , Eichler E.E. , Schwartz S. , Nicholls R.D. ( 2000 ) Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10 : 597 – 610 . ↵ Jurka J. ( 1998 ) Repeats in genomic DNA: mining...
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METHODS: Detecting and Analyzing DNA Sequencing Errors: Toward a Higher Quality of the Bacillus subtilis Genome Sequence
- Claudine Médigue,
- Matthias Rose,
- Alain Viari,
- and Antoine Danchin
Genome Res. November 1, 1999 9: 1116-1127; doi:10.1101/gr.9.11.1116
...of bacteria. Microbiol. Rev. 57 : 543 – 594 . ↵ Richterich P. ( 1998 ) Estimation of errors in “raw” DNA sequences: A validation study. Genome Res. 8 : 251 – 259 . ↵ Salzberg S.L. , Delcher A.L. , Kasif S. , White O. ( 1998 ) Microbial gene identification using interpolated Markov models. Nucleic Acids Res...

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