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RESOURCE: Mapping short DNA sequencing reads and calling variants using mapping quality scores
- Heng Li,
- Jue Ruan,
- and Richard Durbin
Genome Res. November 2008 18: 1851-1858; Published in Advance August 19, 2008, doi:10.1101/gr.078212.108
.... This is analogous to calling a consensus from a sequence assembly, and we propose a Bayesian approach to this issue that is related to that used in assembly software CAP3 ( Huang and Madan 1999 ). In summary, this article presents methods and software for mapping short sequence reads to a reference , calculating...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
...across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
...genes may map to multiple unigenes representing the same gene, which may lead to artificially high levels of contamination. MGT completeness significantly improved after the CAP3 assembly step (see Supplemental Material), which resulted in 74 MGTs with completeness higher than 50% and 131 MGTs...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
..., stromal cells, SMCs, neurons, and immune cells (e.g., B cells in humans and monkeys and macrophages in mouse). We found similar expression patterns of the marker genes in the same cell types, such as PGC and CLDN18 in epithelial cells, COL3A1 and COL1A2 in stromal cells, and JCHAIN and CAP3 in immune...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...MEIs in three-generation pedigreesBlood-derived DNA samples from 599 individuals in 33 three-generation pedigrees were whole- sequenced at an average depth of ∼30× using Illumina paired-end technology (Supplemental Table S1). In these pedigrees, we designate the grandparents as generation 1...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...and are closely connected to other processes shaping mRNA expression, from the transcription process itself to 5′ end capping, 3′ end cleavage, and mRNA decay (Bentley 2014; Herzel et al. 2017). Moreover, splicing and transcription can influence one another to yield splicing-dependent transcriptional pausing...
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Method: Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
- Xiaohan Yang,
- Timothy J. Tschaplinski,
- Gregory B. Hurst,
- Sara Jawdy,
- Paul E. Abraham,
- Patricia K. Lankford,
- Rachel M. Adams,
- Manesh B. Shah,
- Robert L. Hettich,
- Erika Lindquist,
- Udaya C. Kalluri,
- Lee E. Gunter,
- Christa Pennacchio,
- and Gerald A. Tuskan
Genome Res. April 2011 21: 634-641; Published in Advance March 2, 2011, doi:10.1101/gr.109280.110
...are transcribed and/or under purifying selection. Genome Res 17: 632–640. Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH. 2010. sORF finder: A program package to identify small open reading frames with high coding potential. Bioinformatics 26: 399–400. Huang X, Madan A. 1999. CAP3: A DNA sequence...
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Methods: Gene discovery and annotation using LCM-454 transcriptome sequencing
- Scott J. Emrich,
- W. Brad Barbazuk,
- Li Li,
- and Patrick S. Schnable
Genome Res. January 2007 17: 69-73; Published in Advance November 9, 2006, doi:10.1101/gr.5145806
.... , Zhou, D.X. ( 2005 ) Regulation of meristem activity by chromatin remodelling . Trends Plant Sci. 10 : 332 – 338 . ↵ Huang, X. , Madan, A. ( 1999 ) CAP3: A DNA sequence assembly program . Genome Res. 9 : 868 – 877 . ↵ Kerk, N.M. , Ceserani, T. , Tausta, S.L. , Sussex, I.M. , Nelson, T.M. ( 2003 ) Laser...
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LETTER: Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
- Jinsheng Lai,
- Nrisingha Dey,
- Cheol-Soo Kim,
- Arvind K. Bharti,
- Stephen Rudd,
- Klaus F.X. Mayer,
- Brian A. Larkins,
- Philip Becraft,
- and Joachim Messing
Genome Res. October 2004 14: 1932-1937; doi:10.1101/gr.2780504
.... A total of 23,348 successful sequence reads were obtained and deposited into GenBank. Computational Analysis All sequences were assembled using the CAP3 computer program ( Huang and Madan 1999 ) with the parameters set at 95% identity over 40 bp. The maize cDNA sequence assemblies were imported...
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Method: Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
- Lena Tasse,
- Juliette Bercovici,
- Sandra Pizzut-Serin,
- Patrick Robe,
- Julien Tap,
- Christophe Klopp,
- Brandi L. Cantarel,
- Pedro M. Coutinho,
- Bernard Henrissat,
- Marion Leclerc,
- Joël Doré,
- Pierre Monsan,
- Magali Remaud-Simeon,
- and Gabrielle Potocki-Veronese
Genome Res. November 2010 20: 1605-1612; Published in Advance September 14, 2010, doi:10.1101/gr.108332.110
...,762 contigable reads. Read assembly was done using CAP3 (Huang and Madan 1999), a DNA Sequence Assembly Program, and resulted in 106 contigs sizing between 113 bp and 51,798 bp, covering in total 1,002,117 Tasse et al. 1610 Genome Research www..org bp. Ninety-eight percent of the sequenced nucleotides were...

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