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. 2008 Jul 1;36(Web Server issue):W85-90.
doi: 10.1093/nar/gkn220. Epub 2008 Apr 29.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

Vegeir Knudsen  1 , Gustavo Caetano-Anollés
Affiliations

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

Vegeir Knudsen et al. Nucleic Acids Res. .

Abstract

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement.

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Figures

Figure 1.
Figure 1.
An illustration of the NOBAI software package. (A) A sketch of how the secondary structure of RNA molecules can be used to reconstruct the evolutionary history of organisms. H, hairpin; Sx, stem number x; SSx, substructure number x; Mx, molecule number x; F, the Frobenius norm; Q, Shannon entropy; P, base-pairing propensity and S, mean stem length. (B) A sketch of the processing performed by MARTEN and STOAT (the two main programs in the NOBAI package). (C) A sketch of the processing performed by STRINGGEN and OMROKGEN.
Figure 2.
Figure 2.
Two examples of web pages of the NOBAI web server. (A) Capture of the MARTEN web interface with the default parameters. A brief description of the input parameters can be found under the ‘Documentation’ hyperlink. (B) Capture of a temporary result page generated by the MARTEN web interface. The result files can either be downloaded as separate files or as a compressed tar file.
Figure 3.
Figure 3.
Character data matrix produced by STOAT in NEXUS format (_l.nex file) from 5S rRNA archaeal structures (A) and strict consensus phylogenetic tree reconstructed using PAUP* using maximum parsimony as the optimality criterion. (B). Note that only a top segment of the NEXUS file is shown and that the 5S rRNA sequences are provided as sample input data in the web server.
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