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Resource: The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy,
- Delphine Dauga,
- Fabrice Daian,
- Daniel Sobral,
- François Robin,
- Pierre Khoueiry,
- David Salgado,
- Vanessa Fox,
- Danièle Caillol,
- Renaud Schiappa,
- Baptiste Laporte,
- Anne Rios,
- Guillaume Luxardi,
- Takehiro Kusakabe,
- Jean-Stéphane Joly,
- Sébastien Darras,
- Lionel Christiaen,
- Magali Contensin,
- Hélène Auger,
- Clément Lamy,
- Clare Hudson,
- Ute Rothbächer,
- Michael J. Gilchrist,
- Kazuhiro W. Makabe,
- Kohji Hotta,
- Shigeki Fujiwara,
- Nori Satoh,
- Yutaka Satou,
- and Patrick Lemaire
Genome Res. October 2010 20: 1459-1468; Published in Advance July 20, 2010, doi:10.1101/gr.108175.110
.... Transcript models sharing at least one full exonwere grouped into 20,915 ANISEEDv3.0 genemodels by applying a published clustering algorithm (Gilchrist et al. 2004). Halocynthia roretzi transcript models were generated assembling 60,000 expressed sequences (ESTs, cDNAs) into contigs (Huang and Madan 1999...
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RESOURCE: Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
- Melody S. Clark,
- Yvonne J.K. Edwards,
- Dan Peterson,
- Sandra W. Clifton,
- Amanda J. Thompson,
- Masahide Sasaki,
- Yutaka Suzuki,
- Kiyoshi Kikuchi,
- Shugo Watabe,
- Koichi Kawakami,
- Sumio Sugano,
- Greg Elgar,
- and Stephen L. Johnson
Genome Res. December 2003 13: 2747-2753; Published in Advance January 1, 2003, doi:10.1101/gr.1691503
...subsequently BLAST searched against the Fugu data. Of the latter, all mapped to unique locations in the , frequently 5′ to known genes, indicating their potential as 5′ UTRs. Comparison of Fugu EST Clusters to Zebrafish EST Assemblies With the sequencing of the zebrafish and the current availability of a large...
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LETTER: The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
- Ken Inoue,
- Ken Dewar,
- Nicholas Katsanis,
- Lawrence T. Reiter,
- Eric S. Lander,
- Keri L. Devon,
- Dudley W. Wyman,
- James R. Lupski,
- and Bruce Birren
Genome Res. June 1, 2001 11: 1018-1033; doi:10.1101/gr.180401
...are required to elucidate the nature of these repeat structures involving multiple loci in the . BLAST searches of this 6.6-kb region against the human EST database revealed a number of clones homologous to this portion of the LCRA1 low copy repeat. There are two different genes or groups of genes; one...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...and Nematostella share only two miRNAs, their targets are not conserved, and the low coverage of the EST data set allowed prediction of only 28 putative targets for Hydra-specific miRNAs at a prediction score threshold of 2.5. Nevertheless, we detected specific cleavage products for two of the five mRNAs tested...
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Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
- Konstantinos Kritsas,
- Samuel E. Wuest,
- Daniel Hupalo,
- Andrew D. Kern,
- Thomas Wicker,
- and Ueli Grossniklaus
Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
...% to 98%, with an average of 87.7%. Twenty-two were found in intergenic regions and 14 in introns. All ULEs were screened against Arabidopsis ESTs and novel transcripts detected after exosome depletion (Chekanova et al. 2007). For 28/36 ULEs there was no evidence of transcription, while the remaining...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...able to map one copy and speculated the remaining copies (which they inferred on the basis of cDNA and EST data) to lie in a gap between two clones, RP23-231P12 and RP23-20A22. This gap is closed in our sequence, and no such copies are found. None of the cDNAs or ESTs they attribute to these genes...
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LETTER: Retroposed Copies of the HMG Genes: A Window to Genome Dynamics
- Liora Z. Strichman-Almashanu,
- Michael Bustin,
- and David Landsman
Genome Res. May 1, 2003 13: 800-812; doi:10.1101/gr.893803
...-binding domain to the SP100 nuclear antigen ( Rogalla et al. 2000 ). Retroposed copies of known genes present us with a unique tool to investigate dynamics and function, to learn about the process of retrotransposition, to use as complementary information to ESTs and cDNAs by representing a variety...
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LETTER: Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery
- Daniel G. Peterson,
- Stefan R. Schulze,
- Erica B. Sciara,
- Scott A. Lee,
- John E. Bowers,
- Alexander Nagel,
- Ning Jiang,
- Deanne C. Tibbitts,
- Susan R. Wessler,
- and Andrew H. Paterson
Genome Res. May 1, 2002 12: 795-807; Published in Advance April 12, 2002, doi:10.1101/gr.226102
...sequence quality criteria (i.e., Ph/Pr value &gt;16 over 300 continuous bases, high-quality insert sequence ≥50 bp). The (253 + 409 + 499 = 1161) “quality clones” were BLAST ed against the GenBank Nr (nonredundant), GenBank EST, and SUCEST Sugarcane EST ( http://sucest.lbi.dcc.unicamp.br/en/ ) databases...
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PERSPECTIVE: Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience
- Timothy P. O'Brien,
- Carol J. Bult,
- Christoph Cremer,
- Michael Grunze,
- Barbara B. Knowles,
- Jörg Langowski,
- James McNally,
- Thoru Pederson,
- Joan C. Politz,
- Ana Pombo,
- Günter Schmahl,
- Joachim P. Spatz,
- and Roel van Driel
Genome Res. June 2003 13: 1029-1041; Published in Advance May 12, 2003, doi:10.1101/gr.946403
...of a relatively small number of key genes that play a role in endomesodermal specification during the early development of the sea urchin embryo ( Fig. 5 ; see Davidson et al. 2002 ). Thus, a long-term goal that will require an interdisciplinary approach is to acquire sufficient information to be able to overlay...

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