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PMID: 11937640 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.

Nucleic acids research ·Vol. 30 ·No. 8 ·2002-04-15 ·Pages 1851-8

Graber JH, McAllister GD, Smith TF

Abstract

We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.

MeSH Terms
3' Untranslated Regions Base Sequence Genes, Fungal Markov Chains RNA 3' End Processing RNA, Fungal/analysis RNA, Messenger/metabolism Saccharomyces cerevisiae/genetics Sensitivity and Specificity
Chemicals
3' Untranslated Regions RNA, Fungal RNA, Messenger
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Graber Joel H
Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA. [email protected]
McAllister Gregory D
Smith Temple F
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/30.8.1851
Email
[email protected]
Published
2002-04-15
Pages
1851-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC113205
Subset
IM
Grants
NHLBI NIH HHS · U01 HL066678 · United States
NHLBI NIH HHS · U01 HL66678 · United States
External Links
PubMed source DOI: 10.1093/nar/30.8.1851 PMC Full Text View journal details
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