• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of compfungenJournal's HomeManuscript SubmissionAims and ScopeAuthor GuidelinesEditorial BoardHome
Comp Funct Genomics. Jun 2001; 2(3): 143–154.
PMCID: PMC2447204

A Re-Annotation of the Saccharomyces Cerevisiae Genome

Abstract

Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described. 370 ORFs are defined as totally spurious ORFs which should be disregarded. At least a further 193 genes could be described as very hypothetical, based on a number of criteria. It was found that disparate genes with sequence overlaps over ten amino acids (especially at the N-terminus) are rare in both S. cerevisiae and Sz. pombe. A new S. cerevisiae gene number estimate with an upper limit of 5804 is proposed, but after the removal of very hypothetical genes and pseudogenes this is reduced to 5570. Although this is likely to be closer to the true upper limit, it is still predicted to be an overestimate of gene number. A complete list of revised gene coordinates is available from the Sanger Centre (S. cerevisiae reannotation: ftp://ftp/pub/yeast/SCreannotation).

Full Text

The Full Text of this article is available as a PDF (116K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Bucher P, Bairoch A. A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. Proc Int Conf Intell Syst Mol Biol. 1994;2:53–61. [PubMed]
  • Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 1999 Jan 1;27(1):49–54. [PMC free article] [PubMed]
  • Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 1999 Jan 1;27(1):260–262. [PMC free article] [PubMed]
  • Birney E, Thompson JD, Gibson TJ. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res. 1996 Jul 15;24(14):2730–2739. [PMC free article] [PubMed]
  • DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997 Oct 24;278(5338):680–686. [PubMed]
  • Dujon B. The yeast genome project: what did we learn? Trends Genet. 1996 Jul;12(7):263–270. [PubMed]
  • Gaillardin C, Duchateau-Nguyen G, Tekaia F, Llorente B, Casaregola S, Toffano-Nioche C, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, et al. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes. FEBS Lett. 2000 Dec 22;487(1):134–149. [PubMed]
  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, et al. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546–567. [PubMed]
  • Hieter P, Boguski M. Functional genomics: it's all how you read it. Science. 1997 Oct 24;278(5338):601–602. [PubMed]
  • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955–964. [PMC free article] [PubMed]
  • Mackiewicz P, Kowalczuk M, Gierlik A, Dudek MR, Cebrat S. Origin and properties of non-coding ORFs in the yeast genome. Nucleic Acids Res. 1999 Sep 1;27(17):3503–3509. [PMC free article] [PubMed]
  • Malpertuy A, Tekaia F, Casarégola S, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E, Brottier P, de Montigny J, et al. Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett. 2000 Dec 22;487(1):113–121. [PubMed]
  • Oliver SG. From DNA sequence to biological function. Nature. 1996 Feb 15;379(6566):597–600. [PubMed]
  • Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, et al. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]
  • Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000 Oct;16(10):944–945. [PubMed]
  • Sharp PM, Cowe E. Synonymous codon usage in Saccharomyces cerevisiae. Yeast. 1991 Oct;7(7):657–678. [PubMed]
  • Sonnhammer EL, Durbin R. A workbench for large-scale sequence homology analysis. Comput Appl Biosci. 1994 Jun;10(3):301–307. [PubMed]
  • Stoesser G, Tuli MA, Lopez R, Sterk P. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 1999 Jan 1;27(1):18–24. [PMC free article] [PubMed]
  • Xiang Z, Moore K, Wood V, Rajandream MA, Barrell BG, Skelton J, Churcher CM, Lyne MH, Devlin K, Gwilliam R, et al. Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal to his5. Yeast. 2000 Nov;16(15):1405–1411. [PubMed]
  • Zhang CT, Wang J. Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res. 2000 Jul 15;28(14):2804–2814. [PMC free article] [PubMed]

Articles from Comparative and Functional Genomics are provided here courtesy of Hindawi Publishing Corporation

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...