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Novel Tools for Plant Genome Annotation and Applications to Arabidopsis and Rice

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7. References

  • The Arabidopsis Genome Initiative, 2000, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature 408:796–815.

    Google Scholar 

  • Brendel, V., 2002, Integration of data management and analysis for genome research. In S. Schubert, B. Reusch and N. Jesse (eds.), “Informatik bewegt”. Lecture Notes in Informatics (LNI) — Proceedings P-20:10–21.

    Google Scholar 

  • Brendel, V., and Zhu, W., 2002, Computational modeling of gene structure in Arabidopsis thaliana, Plant Mol. Biol. 48:49–58.

    Article  PubMed  CAS  Google Scholar 

  • Campbell, A.M., and Karlin, S., 2003, Evolution of genome structures, Theor. Pop. Biol. 61:365–366.

    Article  Google Scholar 

  • Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W., 1998, A computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Res. 8:967–974.

    PubMed  CAS  Google Scholar 

  • Haas, B., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K. Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L., and White, O., 2003, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucl. Acids Res. 31:5654–5666.

    Article  PubMed  CAS  Google Scholar 

  • Haas, B.J., Volfovsky, N., Town, C.D., Troukhan, M., Alexandrov, N., Feldman, K.A., Flavell, R.B., White, O., and Salzberg, S.L., 2002, Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 3:research0029.1–0029.12.

    Google Scholar 

  • Huang, X., Adams, M.D., Zhou, H., and Kerlavage, A.R., 1997, A tool for analyzing and annotating genomic sequences, Genomics 46:37–45.

    Article  PubMed  CAS  Google Scholar 

  • Kent, W.J., 2002, BLAT—the BLAST-like alignment tool, Genome Res. 12:656–664.

    Article  PubMed  CAS  MathSciNet  Google Scholar 

  • Konopka, A., 2003, Selected dreams and nightmares about computational biology, Comp. Biol. & Chem. 27:91–92.

    Article  CAS  Google Scholar 

  • Korning, P.G., Hebsgaard, S.M., Rouzé, P., and Brunak, S., 1996, Cleaning the GenBank Arabidopsis thaliana data set, Nucl. Acids Res. 24:316–320.

    Article  PubMed  CAS  Google Scholar 

  • The National Plant Genomics Initiative: objectives for 2003–2008, Plant Physiol. 130:1741–1744.

    Google Scholar 

  • Pavy, N., Rombauts, S., Déhais, P., Mathé, C., Ramana, D.V., Leroy, P., and Rouzé, P., 1999, Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences, Bioinformatics 15:887–899.

    Article  PubMed  CAS  Google Scholar 

  • Schlueter, S.D., Dong, Q., and Brendel, V., 2003, GeneSeqer@PlantGDB—gene structure prediction in plant genomes, Nucl. Acids Res. 31:3597–3600.

    Article  PubMed  CAS  Google Scholar 

  • Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., et al., 2002, Functional annotation of a full-length Arabidopsis cDNA collection, Science 296:141–145.

    Article  PubMed  ADS  Google Scholar 

  • Usuka, J., Zhu, W., and Brendel, V., 2000, Optimal spliced alignment of homologous cDNA to a genomic DNA template, Bioinformatics 16:203–211.

    Article  PubMed  CAS  Google Scholar 

  • Wheelan, S.J., Church, D.M., and Ostell, J.M., 2001, Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 11:1952–1957.

    PubMed  CAS  Google Scholar 

  • Wortman, J., Haas, B.J., Hannick, L.I., Smith, R.K. Jr., Maiti, R., Ronning, C.M., Chan, A.P., Yu, C., Ayele, M., Whitelaw, C.A., White, O.R., and Town, C.D., 2003, Annotation of the Arabidopsis genome, Plant Physiol. 132:461–468.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, W., and Brendel, V., 2003, Identification, characterization, and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome, Nucl. Acids Res. 31:4561–4572.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, W., Schlueter, S.D., and Brendel, V., 2003, Refined annotation of the Arabidopsis thaliana genome by complete EST mapping, Plant Physiol. 132:469–484.

    Article  PubMed  CAS  Google Scholar 

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Brendel, V. (2005). Novel Tools for Plant Genome Annotation and Applications to Arabidopsis and Rice. In: Gustafson, J.P., Shoemaker, R., Snape, J.W. (eds) Genome Exploitation. Springer, Boston, MA. https://doi.org/10.1007/0-387-24187-6_5

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