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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
...user environment for execution of many analyses, without really providing a model for annotation per se. More recently, tools such as PowerBlast (Zhang and Madden 1997) have added a basic notion of annotation to their analytical foundation, allowing display and export of results as features along...
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Letter: EbEST: An Automated Tool Using Expressed Sequence Tags to Delineate Gene Structure
- Jian Jiang and
- Howard J. Jacob
Genome Res. March 1, 1998 8: 268-275; doi:10.1101/gr.8.3.268
....G. and D. Landsman. 1997. A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res. 25: 1626–1632. Zhang, J. and T.L. Madden. 1997. PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7: 649–656. Received...
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LETTER: Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus
- Michael J. Higgins,
- Colleen D. Day,
- Nancy J. Smilinich,
- L. Ni,
- Paul R. Cooper,
- Norma J. Nowak,
- Chris Davies,
- Pieter J. de Jong,
- Fielding Hejtmancik,
- Glen A. Evans,
- Richard J.H. Smith,
- and Thomas B. Shows
Genome Res. January 1, 1998 8: 57-68; doi:10.1101/gr.8.1.57
...into contigs using Phrap (P. Green). Genomic DNA sequence was assessed for gene coding potential using the client program PowerBLAST ( ftp://ncbi.nlm.nih.gov/pub/sim2/PowerBLAST/ ) and a network version of GRAIL ( http://avalon.emp.ornl.gov/GRAIL-bin/EmptyGrailForm ). The latter web page provided...
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RESEARCH: Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6
- M. Ali Ansari-Lari,
- John C. Oeltjen,
- Scott Schwartz,
- Zheng Zhang,
- Donna M. Muzny,
- Jing Lu,
- James H. Gorrell,
- A. Craig Chinault,
- John W. Belmont,
- Webb Miller,
- and Richard A. Gibbs
Genome Res. January 1, 1998 8: 29-40
...) Recognizing exons in genomic sequence using GRAIL II. in Genetic engineering: Principles and methods , ed Setlow J. ( Plenum Press , New York, NY ), 16 : 241 – 253 . ↵ Zhang J. , Madden T.L. ( 1997 ) PowerBLAST: A new network BLAST application for interactive automated sequence analysis and annotation. Genome...
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RESOURCE: An Effective Approach for Analyzing “Prefinished” Genomic Sequence Data
- Peter M. Kuehl,
- Jane M. Weisemann,
- Jeffrey W. Touchman,
- Eric D. Green,
- and Mark S. Boguski
Genome Res. February 1, 1999 9: 189-194; doi:10.1101/gr.9.2.189
...: 241 – 253 . ↵ Zhang J. , Madden T.L. ( 1997 ) PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7 : 649 – 656 . ↵ Zhang M.Q. ( 1997 ) Identification of protein coding regions in the human by quadratic discriminant analysis. Proc...
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Research: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
- Shaofang Li,
- Lee E. Vandivier,
- Bin Tu,
- Lei Gao,
- So Youn Won,
- Shengben Li,
- Binglian Zheng,
- Brian D. Gregory,
- and Xuemei Chen
Genome Res. February 2015 25: 235-245; Published in Advance November 20, 2014, doi:10.1101/gr.182238.114
...higher A/T composition (Fig. 3A,B, insets). Such patterns of A/T distribution were also found for annotated exons (Fig. 3C,D) and at Pol II transcription start sites (TSS) or termination sites (TTS) (Fig. 3E,F), although the A/T skew at TSS and TTS sites was not as strong. Nucleosomes, units of chromatin...
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Letter: SeqHelp: A Program to Analyze Molecular Sequences Utilizing Common Computational Resources
- Ming K. Lee,
- Eric D. Lynch,
- and Mary-Claire King
Genome Res. March 1, 1998 8: 306-312; doi:10.1101/gr.8.3.306
.... Uberbacher. 1994. Recognizing exons in genomic sequence using GRAIL II. Genet. Eng. 16: 241–253. Zhang, J.H. and T.L. Madden. 1997. PowerBlast: A new network blast application for interactive or automated sequence analysis and annotation. Genome Res. 7: 649–656. Received September 10, 1997; accepted...
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METHODS: Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences
- Leslie Y.Y. Chen,
- Szu-Hsien Lu,
- Edward S.C. Shih,
- and Ming-Jing Hwang
Genome Res. July 1, 2002 12: 1106-1111; Published in Advance June 18, 2002, doi:10.1101/gr.224502
.... ( 1998 ) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human . Science 280 : 1077 – 1082 . ↵ Zhang J. , Madden T.L. ( 1997 ) PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7 : 649 – 656...
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REPORT: Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7
- James W. Thomas,
- Tyrone J. Summers,
- Shih-Queen Lee-Lin,
- Valerie V. Braden Maduro,
- Jacquelyn R. Idol,
- Stephen D. Mastrian,
- Joseph F. Ryan,
- D. Curtis Jamison,
- and Eric D. Green
Genome Res. May 1, 2000 10: 624-633; doi:10.1101/gr.10.5.624
.... ( 1998 ) Human calumenin gene (CALU): cDNA isolation and chromosomal mapping to 7q32. Genomics 49 : 331 – 333 . ↵ Zhang J. , Madden T.L. ( 1997 ) PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7 : 649 – 656 . Comparative Genome...
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INSIGHT/OUTLOOK: Database Divisions and Homology Search Files: A Guide for the Perplexed
- B.F. Francis Ouellette and
- Mark S. Boguski
Genome Res. October 1, 1997 7: 952-955; doi:10.1101/gr.7.10.952
...J.A. ( 1996 ) Entrez: Molecular biology database and retrieval system. Methods Enzymol. 266 : 141 – 162 . ↵ Zhang J. , Madden T.L. ( 1997 ) PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7 : 649 – 656 . Database Divisions...

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