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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
..., Selaginella moellendorffii, Sphagnum magellanicum, UniProt Pinales and Cupressales, and Swiss-Prot proteomes to the repeat-soft-masked WRC using RepeatMasker v4.0.8 (Smit et al. 2015) with up to 2-kbp extension on both ends. Gene models were predicted using FGENESH+ v3.1.1 (Salamov and Solovyev 2000), FGENESH_EST...
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Research: High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates
- Jun Matsumoto,
- Ken Dewar,
- Jessica Wasserscheid,
- Graham B. Wiley,
- Simone L. Macmil,
- Bruce A. Roe,
- Robert W. Zeller,
- Yutaka Satou,
- and Kenneth E.M. Hastings
Genome Res. May 2010 20: 636-645; Published in Advance March 8, 2010, doi:10.1101/gr.100271.109
...than the TMED5 gene, based on the occurrence of 29 rpL12 59-ESTs and only three TMED5 59-ESTs in the Ciona tailbud embryo conventional cDNA EST library of Satou et al. (2003) (http://hoya.zool.kyoto-u.ac.jp/ download.html). This suggests a >1000-fold preferential derivation of SL-PCR products from TMED...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...). Table 2. Summary statistics for the fly s Genome #Seqs Max Min Mean Median GC% Est. length (Mb) NG50 Dist to dm3 Drosophila melanogaster dm3 15 29,004,656 19,517 12,027,821 6,668,899 41.7 176 a 23,011,544 0 D. pseudoobscura dp4 4896 30,794,189 101 31,202 1734 45.2 161 a 11,692,001 0.439806 D. ananassae...
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Research: High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation
- E. Josephine Clowney,
- Angeliki Magklara,
- Bradley M. Colquitt,
- Nidhi Pathak,
- Robert P. Lane,
- and Stavros Lomvardas
Genome Res. August 2011 21: 1249-1259; Published in Advance June 24, 2011, doi:10.1101/gr.120162.110
...regulatory modules that are responsible for OR expression in the MOE, we looked for common Figure 1. One thousand eighty-five olfactory receptor 59 structures mapped by high-throughput RLM-RACE. For selected ORs (A–D), RefSeq records (green), ESTs (purple), summary hybridization patterns and computed exons...
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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
...to compare different conditions rapidly and to assay essential genes opens the door to high-throughput, -scale examination of bacterial responses to various stressors. This approach can be applied to any question in which the evaluation of bacterial fitness is important.MethodsTraDIS-Xpress: a refined...
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LETTER: Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
- Li Li,
- Brian P. Brunk,
- Jessica C. Kissinger,
- Deana Pape,
- Keliang Tang,
- Robert H. Cole,
- John Martin,
- Todd Wylie,
- Mike Dante,
- Steven J. Fogarty,
- Daniel K. Howe,
- Paul Liberator,
- Carmen Diaz,
- Jennifer Anderson,
- Michael White,
- Maria E. Jerome,
- Emily A. Johnson,
- Jay A. Radke,
- Christian J. Stoeckert, Jr.,
- Robert H. Waterston,
- Sandra W. Clifton,
- David S. Roos,
- and L. David Sibley
Genome Res. March 1, 2003 13: 443-454; doi:10.1101/gr.693203
...Maria E Jerome Fogarty DK Howe Daniel K Howe Diaz, C Johnson, E.A Fogarty, S.J Waterston, Robert H White Roos Jennifer Howe Daniel K. Brian Brunk genome;13/3/443 1549-5469 10.1101/gr.693203 1088-9051 Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene...
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RESEARCH: Analysis of EST-Driven Gene Annotation in Human Genomic Sequence
- L. Charles Bailey, Jr.,
- David B. Searls,
- and G. Christian Overton
Genome Res. April 1, 1998 8: 362-376; doi:10.1101/gr.8.4.362
...al. 1997 ; Wolfsberg and Landsman 1997 ). Such information may be used not only to further biologic evaluation of specific genes, but as the basis for preliminary investigations of -wide structure and function. RESULTS Construction of Genomic Test Sets To assess the effectiveness of ESTs as a probe...
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Methods: The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
- Yi Xing,
- Alissa Resch,
- and Christopher Lee
Genome Res. March 2004 14: 426-441; Published in Advance February 12, 2004, doi:10.1101/gr.1304504
...adaptation index. RESULTS Isoform Generation for Transcobalamin I (TCN1) We used the TCN1 gene (UniGene cluster Hs.2012) as an example to show the isoform construction process. Figure 4 summarizes the raw input data: alignment of all the mRNA and EST sequences in Hs.2012 to its genomic region...
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Letter: Kaleidaseq: A Web-Based Tool to Monitor Data Flow in a High Throughput Sequencing Facility
- Neilay N. Dedhia and
- W. Richard McCombie
Genome Res. March 1, 1998 8: 313-318; doi:10.1101/gr.8.3.313
...-tagged site (STSs), expressed sequence tags (ESTs), and cDNAs, are sequenced concurrently. Typically, there are lag times of days between the preparing of plaques and final processing of the sequenced samples. During this time decisions need to be made about scheduling of the various steps and allocation...
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Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
- Tsung-Cheng Chang,
- Mihaela Pertea,
- Sungyul Lee,
- Steven L. Salzberg,
- and Joshua T. Mendell
Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
...RNA transcript assemblies (Supplemental Figs. S12, S13). These findings demonstrate that production of individual miRNAs in polycistronic clusters can be uncoupled through the use of alternative promoters. Alternative splicing A previous analysis of existing expressed sequence tags (ESTs) and mRNAs revealed...

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