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 Furuno, M. Articles by Okazaki, Y. Search for Related Content PubMed PubMed Citation Articles by Furuno, M. Articles by Okazaki, Y. Pubmed/NCBI databases Compound via MeSH Substance via MeSH Social Bookmarking                   What's this?

Letter

CDS Annotation in Full-Length cDNA Sequence

¹Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ²Multimedia Development Center, Advanced Technology Development Department, NTT Software Corporation, Naka-ku, Yokohama, Kanagawa 231-8554, Japan ³Institute for Advanced Biosciences, Keio University, Tsuruoka-city, Yamagata, 997-0017, Japan ⁴Mouse Genome Informatics Group, The Jackson Laboratory, Bar Harbor, Maine 04609, USA ⁵Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.

⁶ Corresponding author.
E-MAIL rgscerg{at}gsc.riken.go.jp; FAX 81-45-503-9216.

[Supplemental material is 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:

				L. Kong, Y. Zhang, Z.-Q. Ye, X.-Q. Liu, S.-Q. Zhao, L. Wei, and G. Gao CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine Nucleic Acids Res., July 13, 2007; 35(suppl_2): W345 - W349. [Abstract] [Full Text] [PDF]

				J. Ponjavic, C. P. Ponting, and G. Lunter Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs Genome Res., May 1, 2007; 17(5): 556 - 565. [Abstract] [Full Text] [PDF]

				Z. Xiong, E. Liu, Y. Yan, R. T. Silver, F. Yang, I. H. Chen, Y. Chen, S. Verstovsek, H. Wang, J. Prchal, et al. An Unconventional Antigen Translated by a Novel Internal Ribosome Entry Site Elicits Antitumor Humoral Immune Reactions J. Immunol., October 1, 2006; 177(7): 4907 - 4916. [Abstract] [Full Text] [PDF]

				T. Ravasi, H. Suzuki, K. C. Pang, S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M. C. Frith, M. M. Gongora, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome Genome Res., January 1, 2006; 16(1): 11 - 19. [Abstract] [Full Text] [PDF]

				S. D. Drabenstot, D. M. Kupfer, J. D. White, D. W. Dyer, B. A. Roe, K. L. Buchanan, and J. W. Murphy FELINES: a utility for extracting and examining EST-defined introns and exons Nucleic Acids Res., November 15, 2003; 31(22): e141 - e141. [Abstract] [Full Text] [PDF]