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RESEARCH: GAIA: Framework Annotation of Genomic Sequence
- L. Charles Bailey, Jr.,
- Stephen Fischer,
- Jonathan Schug,
- Jonathan Crabtree,
- Mark Gibson,
- and G. Christian Overton
Genome Res. March 1, 1998 8: 234-250; doi:10.1101/gr.8.3.234
...community as well, in developing a coherent approach to -scale annotation. Initial Sensors The CARTA prototype currently includes five senBAILEY ET AL. 240 GENOME RESEARCH sors, three of which perform similarity searches, one of which invokes a pattern-matching gene finder, and one of which attempts...
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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
...., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002 . Whole- shotgun assembly and analysis of the of Fugu rubripes. Science 297 : 1301 -1310. ↵ Bailey Jr., L.C., Searls, D.B., and Overton, G.C. 1998 . Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8 : 362 -376. ↵ Bairoch...
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RESOURCE: GANESH: Software for Customized Annotation of Genome Regions
- Derek Huntley,
- Holger Hummerich,
- Damian Smedley,
- Sasivimol Kittivoravitkul,
- Mark McCarthy,
- Peter Little,
- and Marek Sergot
Genome Res. September 2003 13: 2195-2202; doi:10.1101/gr.698103
...., Myers, E.W., and Lipman, D.J. 1990 . Basic local alignment search tool. J. Mol. Biol. 215 : 403 –410. ↵ Bailey Jr., L.C., Searls, D.B., and Overton, G.C. 1998 . Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8 : 362 –376. ↵ Bateman, A., Birney, E., Cerruti, L., Durbin, R...
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RESOURCE: PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
- Scott Schwartz,
- Zheng Zhang,
- Kelly A. Frazer,
- Arian Smit,
- Cathy Riemer,
- John Bouck,
- Richard Gibbs,
- Ross Hardison,
- and Webb Miller
Genome Res. April 1, 2000 10: 577-586; doi:10.1101/gr.10.4.577
...) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8 : 362 – 376 . ↵ Battey J. , Jordan E. , Cox D. , Dove W. ( 1999 ) An action plan for mouse genomics. Nat. Genet. 21 : 73 – 75 . ↵ Blattner F.R. , Plunkett G. , III , Bloch C.A. , Perna N.T. , Burland V. , Riley M. , Collado...
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GENOME METHODS: A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
- Liliana Florea,
- George Hartzell,
- Zheng Zhang,
- Gerald M. Rubin,
- and Webb Miller
Genome Res. September 1, 1998 8: 967-974; doi:10.1101/gr.8.9.967
....C. , Jr. , Searls D.B. , Overton G.C. ( 1998 ) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8 : 362 – 376 . ↵ Birney E. , Durbin R. ( 1997 ) Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Proc. Fifth Int. Conf...
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Methods: A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
- The Ludwig–FAPESP Transcript Finishing Initiative,
- Mari Cleide Sogayar,
- and Anamaria A. Camargo
Genome Res. July 2004 14: 1413-1423; Published in Advance June 14, 2004, doi:10.1101/gr.2111304
...as for the delineation of gene boundaries and alternatively spliced isoforms. Footnotes [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. CF272536–CF272733.] ↵ 3 Ludwig Institute for Cancer Research...
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METHODS: Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics
- Chun-Hung Lai,
- Chang-Yuan Chou,
- Lan-Yang Ch'ang,
- Chung-Shyan Liu,
- and Wen-chang Lin
Genome Res. May 1, 2000 10: 703-713; doi:10.1101/gr.10.5.703
....B. , Overton G.C. ( 1998 ) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8 : 362 – 376 . ↵ Banfi S. , Borsani G. , Bulfone A. , Ballabio A. ( 1997 ) Drosophila-related expressed sequences. Hum. Mol. Genet. 6 : 1745 – 1753 . ↵ Banfi S. , Borsani G. , Rossi E. , Bernard L...

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