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. 2005 Jul 1;33(Web Server issue):W650-3.
doi: 10.1093/nar/gki473.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Jakob H Havgaard  1 , Rune B Lyngsø, Jan Gorodkin
Affiliations

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Jakob H Havgaard et al. Nucleic Acids Res. .

Abstract

Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at http://foldalign.kvl.dk.

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Figures

Figure 1
Figure 1
An example of the output from a scan comparison. The sequences contain one tRNA each. The tRNA structures were taken from the tRNA database and the surrounding sequences from GenBank (14,15). Default parameters were used for the alignment. At the top of the output, there is a plot of the Z-scores. It is followed by a ranked list of non-overlapping local alignments. In the example the two best alignments have been included. The locations of the best hits are marked with bars on the sides of the Z-score plot. The bars of the best hit have a darker blue color than the rest. The final section shows the structures of the best hits.
Figure 2
Figure 2
An example of the output from Local and Global comparisons. The two tRNA sequences were aligned using the Local comparison type with default parameters. The sequences were taken from the tRNA database (14).
See this image and copyright information in PMC

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