Construct a tool for thermodynamic controlled prediction of conserved secondary structure

A tool for prediction of conserved secondary structure of a set of homologous single-stranded RNAs is presented. For each RNA of the set the structure distribution is calculated and stored in a base pair probability matrix. Gaps, resulting from a multiple sequence alignment of the RNA set, are intro...

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Bibliographic Details
Published in:Nucleic acids research 1999-11, Vol.27 (21), p.4208-4217
Main Authors: Rupert, Luck, Stefan, Graf, Gerhard, Steger
Format: Article
Language:English
Subjects:
Algorithms
Animals
Base Pair Mismatch
Base Pairing
Base Sequence
Consensus Sequence - genetics
Conserved Sequence - genetics
Databases, Factual
histones
Humans
Mutation - genetics
Nucleic Acid Conformation
RNA - chemistry
RNA - genetics
RNA - metabolism
RNA, Small Nuclear - genetics
Sequence Alignment
Sequence Homology, Nucleic Acid
snRNA U7
Software
Thermodynamics
User-Computer Interface
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Summary:A tool for prediction of conserved secondary structure of a set of homologous single-stranded RNAs is presented. For each RNA of the set the structure distribution is calculated and stored in a base pair probability matrix. Gaps, resulting from a multiple sequence alignment of the RNA set, are introduced into the individual probability matrices. These ‘aligned’ probability matrices are summed up to give a consensus probability matrix emphasizing the conserved structural elements of the RNA set. Because the multiple sequence alignment is independent of any structural constraints, such an alignment may result in introduction of gaps into the homologous probability matrices that disrupt a common consensus structure. By use of its graphical user interface the presented tool allows the removal of such misalignments, which are easily recognized, from the individual probability matrices by optimizing the sequence alignment with respect to a structural alignment. From the consensus probability matrix a consensus structure is extracted, which is viewable in three different graphical representations. The functionality of the tool is demonstrated using a small set of U7 RNAs, which are involved in 3′ -end processing of histone mRNA precursors. Supplementary Material lists further results obtained. Advantages and drawbacks of the tool are discussed in comparison to several other algorithms.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/27.21.4208