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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...with mate-pair reads followed by gap closure, was performed using Platanus v1.2.4 (Kajitani et al. 2014).Whole sequencing for a male whale shark used the 10x Genomics Chromium to produce Linked-Read data. A DNA library was prepared using 12 ng of gDNA extracted from blood cells according to the user guide...
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LETTER: Large-Scale Concatenation cDNA Sequencing
- Wei Yu,
- Björn Andersson,
- Kim C. Worley,
- Donna M. Muzny,
- Yan Ding,
- Wen Liu,
- Jennifer Y. Ricafrente,
- Meredith A. Wentland,
- Greg Lennon,
- and Richard A. Gibbs
Genome Res. April 1, 1997 7: 353-358; doi:10.1101/gr.7.4.353
...generated from the original clones, utilizing 85 specific oligonucleotide primers for gap closure and complete double-stranded coverage. The resulting sequences were edited to the established community standard of ≥99.99% accuracy. Of a total 1793 sequences obtained for this project, 122 reads (6.8%) were...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...in host–pathogen interactions (Adomako-Ankomah et al. 2016). In that initial study, we used sequence coverage to infer copy number, and we were eager to refine this analysis using the long-read de novo assemblies presented here.The gap closure enabled us to determine the number, order, and orientation...
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ARTICLE: Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.
- M A Ansari-Lari,
- Y Shen,
- D M Muzny,
- W Lee,
- and R A Gibbs
Genome Res. March 1997 7: 268-280; doi:10.1101/gr.7.3.268
...: 1682 – 1687 . Muzny, D.M., S. Richards, Y. Shen, and R.A. Gibbs.1994. PCR based strategies for gap closure in large-scale sequencing projects. In Automated DNA sequencing and analysis (ed. M.D. Adams, C. Fields, and J.C. Venter), pp. 182–190. Academic Press, San Diego, CA. Nagafuchi, S., , Yanagisawa...
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METHODS: Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing
- Michael C. Wendl and
- Robert H. Waterston
Genome Res. December 1, 2002 12: 1943-1949; doi:10.1101/gr.655102
...of gaps must still be closed by directed means. View larger version: In this window In a new window Figure 8. Probability of closure as a function of depth of coverage for various projects: 1. Zhu et al. (1999) ; 2. Dewar et al. (1998) ; 3. Fleischmann et al. (1995) ; 4. McPherson et al. (2001) ; 5. Adams...
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RESEARCH: Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains
- John C. Oeltjen,
- Tracy M. Malley,
- Donna M. Muzny,
- Webb Miller,
- Richard A. Gibbs,
- and John W. Belmont
Genome Res. April 1, 1997 7: 315-329; doi:10.1101/gr.7.4.315
...) 370, 373, 373A, or 377 sequencers. Sequence Assembly and Gap Closure Raw sequence data were transferred to a UNIX platform for editing and assembly. Vector and low-quality data were removed using SEQPREP software developed by the Molecular Biology Computational Resource Center at Baylor College...
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LETTER: Parking Strategies for Genome Sequencing
- Jared C. Roach,
- Vesteinn Thorsson,
- and Andrew F. Siegel
Genome Res. July 1, 2000 10: 1020-1030; doi:10.1101/gr.10.7.1020
...of sequenced clones. A tabulation of the number of gaps in a project as a function of overlap is provided in Table 1 . At infinite time (when a project has reached its jamming limit), the number of gaps decreases monotonically to zero as the allowed overlap increases from zero to fifty percent. If projects...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...end sequences. The average Phred ( Ewing and Green 1998 ; Ewing et al. 1998 ) quality score of the consensus contig sequence is 86.8, with 908,521 bp (91.3%) having the highest Phred Score of 90 and only 1198 bp (0.1%) having a Phred score &lt;20. The total estimated length of the gaps is 15,143 bp...
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METHODS: Analysis of Sequence-Tagged-Connector Strategies for DNA Sequencing
- Andrew F. Siegel,
- Barbara Trask,
- Jared C. Roach,
- Gregory G. Mahairas,
- Leroy Hood,
- and Ger van den Engh
Genome Res. March 1, 1999 9: 297-307; doi:10.1101/gr.9.3.297
...York, NY ), pp 73 – 89 . ↵ Richards S. , Muzny D.M. , Civitello D.M. , Lu F. , Gibbs R.A. Adams M. , Fields C. , Venter J. ( 1994 ) Sequence map gaps and directed reverse sequencing for the completion of large sequencing projects. in Automated DNA sequencing and analysis , eds Adams M. , Fields C...
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LETTER: A Software System for Data Analysis in Automated DNA Sequencing
- Michael C. Giddings,
- Jessica Severin,
- Michael Westphall,
- Jiazhen Wu,
- and Lloyd M. Smith
Genome Res. June 1, 1998 8: 644-665; doi:10.1101/gr.8.6.644
...the Back End into the Front End to provide closure for gaps after initial shotgun sequencing has occurred (e.g., see Fleischmann et al. 1995 ). Significant strides have been made in all of these phases of the sequencing process. Increasingly, Front End steps are being automated by robotic systems ( Wilson...

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