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

Jakob H Havgaard; Rune B Lyngsø; Jan Gorodkin

doi:10.1093/nar/gki473

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

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

Authors

Jakob H Havgaard¹, Rune B Lyngsø, Jan Gorodkin

Affiliation

¹ Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computer Graphics
Internet
Nucleic Acid Conformation
RNA / chemistry*
Sequence Alignment / methods*
Sequence Analysis, RNA / methods*
Software*
User-Computer Interface

Substances

RNA