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Analysis of aligned tRNAs

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posted on 30.12.2011, 16:43 by Björn Voß

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Taken from "Structural analysis of aligned RNAs"

Nucleic Acids Research 2006;34(19):5471-5481.

Published online 04 Oct 2006

PMCID:PMC1636479.

© 2006 The Author(s)

A ClustalW alignment of 10 arbitrarily chosen tRNAs from Rfam was analysed with RNAlishapes. () The consensus structure predicted by RNAlishapes drawn as a squiggle plot using RNAplot from the Vienna RNA package (). The sequence corresponds to the sequence of the most frequent base at each position. Colours indicate different stems (see B). () The alignment produced by ClustalW. Additionally the consensus structure is given on the last line together with the score in parentheses. The different stems are colour coded in the alignment as well as in the consensus structure. Note, that helical regions do not need to have the same length in all sequences. () Output of RNAlishapes, when running in shape probabilistic mode. Four consensus shapes with a probability >10 have been predicted. For each the free energy and the dot-bracket representation of the shrep (both on the first line), the probability of the shape and the shape notation (both on the second line) are computed.

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