Gene prediction

• Mount, D. (2001) Bioinformatics: Sequence and Genome Analysis. Gene Prediction (chapter 8) CSHL Press.
  
  
• M. Burset, I.A. Seledtsov and V.V. Solovyev. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acid Research 28(21):4364-4375.
  
  
• R. Guigó, P. Agarwal, J.F. Abril, M. Burset and J.W. Fickett. (2000) An Assessment of Gene Prediction Accuracy in Large DNA Sequences. Genome Research 10(10):1631-1642.
  
  
• G. Parra, E. Blanco, and R. Guigó. (2000) Geneid in Drosophila. Genome Research 10(4):511-515.
  
  
• M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis. (2000) Genome Annotation Assesment in Drosophila melanogaster. Genome Research 10(4):483-501.
  
  
• Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
  
  
• Burge, C. B. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8, 346-354.
  
  
• M. Burset and R. Guigó. (1996) Evaluation of gene structure prediction programs. Genomics, 34(3):353-357.
  
  

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Synthenia

• T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds and R. Guigó. (2001) SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments. Genome Research 11(9):1574-1583
  
  

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Selenoproteins

• S.C. Low and M.J. Berry (1996) Knowing when not to stop: selenocysteine incorporation in eukaryotes. TIBS, 21, 203-208.
  
  
• R. Walczak, P. Carbon and A. Krol (1998) An essential non-Watson-Crick base pair motif in 3'UTR to mediate selenoprotein translation. RNA, 4, 74-84.
  
  
• S. Castellano, N. Morozova, M. Morey, M.J. Berry, F. Serras, M. Corominas and R. Guigó (2001) in silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO reports, 2(8):697-702.
  
  
• F.J Martin-Romero, G.V. Kryukov, A.V. Lobanov, B.A. Carlson, B.J. Lee, V.N. Gladyshev and D.L. Hatfield (2001) Selenium Metabolism in Drosophila. JBC, 276(32):29798-804.
  
  
• P.R. Copeland, J.E. Fletcher, B.A. Carlson, D.L. Hatfield and D.M. Driscoll (2000) A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs. EMBO Journal, 19, 306-314.