Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
7. References
The Arabidopsis Genome Initiative, 2000, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature 408:796–815.
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.
Brendel, V., and Zhu, W., 2002, Computational modeling of gene structure in Arabidopsis thaliana, Plant Mol. Biol. 48:49–58.
Campbell, A.M., and Karlin, S., 2003, Evolution of genome structures, Theor. Pop. Biol. 61:365–366.
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.
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.
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.
Huang, X., Adams, M.D., Zhou, H., and Kerlavage, A.R., 1997, A tool for analyzing and annotating genomic sequences, Genomics 46:37–45.
Kent, W.J., 2002, BLAT—the BLAST-like alignment tool, Genome Res. 12:656–664.
Konopka, A., 2003, Selected dreams and nightmares about computational biology, Comp. Biol. & Chem. 27:91–92.
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.
The National Plant Genomics Initiative: objectives for 2003–2008, Plant Physiol. 130:1741–1744.
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.
Schlueter, S.D., Dong, Q., and Brendel, V., 2003, GeneSeqer@PlantGDB—gene structure prediction in plant genomes, Nucl. Acids Res. 31:3597–3600.
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.
Usuka, J., Zhu, W., and Brendel, V., 2000, Optimal spliced alignment of homologous cDNA to a genomic DNA template, Bioinformatics 16:203–211.
Wheelan, S.J., Church, D.M., and Ostell, J.M., 2001, Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 11:1952–1957.
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.
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.
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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer Science+Business Media, Inc.
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/0-387-24187-6_5
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-24123-4
Online ISBN: 978-0-387-24187-6
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)