This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Volfovsky, N. Articles by Salzberg, S. L. Search for Related Content PubMed PubMed Citation Articles by Volfovsky, N. Articles by Salzberg, S. L. Social Bookmarking                   What's this?

Methods

Computational Discovery of Internal Micro-Exons

¹ The Institute for Genomic Research, Rockville, Maryland 20850, USA

Very short exons, also known as micro-exons, occur in large numbers in some eukaryotic genomes. Existing annotation tools have a limited ability to recognize these short sequences, which range in length up to 25 bp. Here, we describe a computational method for the identification of micro-exons using near-perfect alignments between cDNA and genomic DNA sequences. Using this method, we detected 319 micro-exons in 4 complete genomes, of which 224 were previously unknown, human (170), the nematode Caenorhabditis elegans (4), the fruit fly Drosophila melanogaster (14), and the mustard plant Arabidopsis thaliana (36). Comparison of our computational method with popular cDNA alignment programs shows that the new algorithm is both efficient and accurate. The algorithm also aids in the discovery of micro-exon-skipping events and cross-species micro-exon conservation.

² Present address: Advanced Biomedical Computing Center, National Cancer Institute-Frederick/SAIC, Frederick, Maryland 21702, USA.

³ Corresponding author.
E-MAIL natalia{at}ncifcrf.gov; FAX (301) 838-0208.

[Supplementary material available online at www.genome.org.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				O. Gotoh A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence Nucleic Acids Res., May 1, 2008; 36(8): 2630 - 2638. [Abstract] [Full Text] [PDF]

				U. Schulze, B. Hepp, C. S. Ong, and G. Ratsch PALMA: mRNA to genome alignments using large margin algorithms Bioinformatics, August 1, 2007; 23(15): 1892 - 1900. [Abstract] [Full Text] [PDF]

				X. Cui, T. Vinar, B. Brejova, D. Shasha, and M. Li Homology search for genes Bioinformatics, July 1, 2007; 23(13): i97 - i103. [Abstract] [Full Text] [PDF]

				M. Zhang and W. Gish Improved spliced alignment from an information theoretic approach Bioinformatics, January 1, 2006; 22(1): 13 - 20. [Abstract] [Full Text] [PDF]

				A. A. Sharov, D. B. Dudekula, and M. S.H. Ko Genome-wide assembly and analysis of alternative transcripts in mouse Genome Res., May 1, 2005; 15(5): 748 - 754. [Abstract] [Full Text] [PDF]

				T. D. Wu and C. K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics, May 1, 2005; 21(9): 1859 - 1875. [Abstract] [Full Text] [PDF]

				T. Masaki, N. Mitsui, H. Tsukagoshi, T. Nishii, A. Morikami, and K. Nakamura ACTIVATOR of Spomin::LUC1/WRINKLED1 of Arabidopsis thaliana Transactivates Sugar-inducible Promoters Plant Cell Physiol., April 1, 2005; 46(4): 547 - 556. [Abstract] [Full Text] [PDF]

				S. Aubourg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, A. Cottet, A. Couloux, P. Dehais, G. Deleage, A. Duclert, et al. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts Nucleic Acids Res., January 1, 2005; 33(suppl_1): D641 - D646. [Abstract] [Full Text] [PDF]

				L. Ding, A. Sabo, N. Berkowicz, R. R. Meyer, Y. Shotland, M. R. Johnson, K. H. Pepin, R. K. Wilson, and J. Spieth EAnnot: A genome annotation tool using experimental evidence Genome Res., December 1, 2004; 14(12): 2503 - 2509. [Abstract] [Full Text] [PDF]

				B. J. Haas, A. L. Delcher, S. M. Mount, J. R. Wortman, R. K. Smith Jr, L. I. Hannick, R. Maiti, C. M. Ronning, D. B. Rusch, C. D. Town, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res., October 1, 2003; 31(19): 5654 - 5666. [Abstract] [Full Text] [PDF]