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Stochastic context-free grammars for tRNA modeling.
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MedLine Citation:
PMID:  7800507     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. Results show that after having been trained on as few as 20 tRNA sequences from only two tRNA subfamilies (mitochondrial and cytoplasmic), the model can discern general tRNA from similar-length RNA sequences of other kinds, can find secondary structure of new tRNA sequences, and can produce multiple alignments of large sets of tRNA sequences. Our results suggest potential improvements in the alignments of the D- and T-domains in some mitochondrial tRNAs that cannot be fit into the canonical secondary structure.
Authors:
Y Sakakibara; M Brown; R Hughey; I S Mian; K Sjölander; R C Underwood; D Haussler
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Nucleic acids research     Volume:  22     ISSN:  0305-1048     ISO Abbreviation:  Nucleic Acids Res.     Publication Date:  1994 Nov 
Date Detail:
Created Date:  1995-01-20     Completed Date:  1995-01-20     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0411011     Medline TA:  Nucleic Acids Res     Country:  ENGLAND    
Other Details:
Languages:  eng     Pagination:  5112-20     Citation Subset:  IM    
Affiliation:
Sinsheimer Laboratories, University of California, Santa Cruz 95064.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Base Sequence
Computer Simulation*
Models, Statistical*
Molecular Sequence Data
Nucleic Acid Conformation*
RNA, Transfer / chemistry*
Sequence Alignment*
Stochastic Processes
Grant Support
ID/Acronym/Agency:
GM17129/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
9014-25-9/RNA, Transfer
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Full Text
Journal Information
Journal ID (nlm-ta): Nucleic Acids Res
ISSN: 0305-1048
ISSN: 1362-4962
Article Information
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Print publication date: Day: 25 Month: 11 Year: 1994
Volume: 22 Issue: 23
First Page: 5112 Last Page: 5120
ID: 523785
PubMed Id: 7800507

Stochastic context-free grammars for tRNA modeling.
Y Sakakibara
M Brown
R Hughey
I S Mian
K Sj?lander
R C Underwood
D Haussler
Sinsheimer Laboratories, University of California, Santa Cruz 95064.



Article Categories:
  • Research Article


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