Positive sample only learning (PSOL) for predicting RNA genes in E. coli

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 535-538

  Meraz, Richard F ^a   He, Xiaofeng ^a   Ding, Chris H Q ^a   Holbrook, Stephen R ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; GENOMIC SEQUENCES; NON-CODING SEQUENCES; POSITIVE SAMPLE ONLY LEARNING (PSOL);

ALGORITHMS; BIOASSAY; CODES (SYMBOLS); COMPUTER PROGRAMMING LANGUAGES; COMPUTER SIMULATION; DATA PROCESSING; DATABASE SYSTEMS; ESCHERICHIA COLI; FREE ENERGY; GENES; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; STATISTICAL METHODS;

RNA;

EID: 14044278169     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (12)

1. R. J. Carter, I. Dubchak, and S. R. Holbrook. A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res, 29(19):3928-38, 2001.
2. S. Chen, E. A. Lesnik, T. A. Hall, R. Sampath, R. H. Griffey, D. J. Ecker, and L. B. Blyn. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems, 65(2-3):157-77, 2002.
3. S. R. Eddy. Noncoding RNA genes. Curr Opin Genet Dev, 9(6):695-9, 1999.
4. V. A. Erdmann, M. Z. Barciszewska, M. Szymanski, A. Hochberg, N. de Groot, and J. Barciszewski. The non-coding RNAs as riboregulators. Nucleic Acids Res, 29(1):189-93, 2001.
5. S. Gottesman, G. Storz, C. Rosenow, N. Majdalani, F. Repoila, and K. M. Wassarman. Small RNA regulators of translation: mechanisms of action and approaches for identifying new small RNAs. Cold Spring Harb Symp Quant Biol, 66:353-62, 2001.
6. S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy. Rfam: an RNA family database. Nucleic Acids Res, 31(1):439-41, 2003.
7. R. Hershberg, S. Altuvia, and H. Margalit. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res, 31(7):1813-20, 2003.
8. R. J. Klein and S. R. Eddy. RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics, 4(1):44, 2003.
9. E. Rivas and S. R. Eddy. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2(1):8, 2001.
10. B. Tjaden, R. M. Saxena, S. Stolyar, D. R. Haynor, E. Kolker, and C. Rosenow. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res, 30(17):3732-8, 2002.
11. V. N. Vapnik. Statistical learning theory. Adaptive and learning systems for signal processing, communications, and control. Wiley, New York, 1998.
12. S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49(2):145-65, 1999.