FOLDALIGN

Department of Genetics
Washington University in St. Louis
School of Medicine

FOLDALIGN server

Wash U. mirror

Introduction

Fasta format

Download software

Man pages

BiRC

Stormo lab

The FOLDALIGN server

NEW VERSION FOR PAIRWISE COMPARISON: http://foldalign.kvl.dk

Description
This server runs a limited version of the FOLDALIGN program. The limitations are in particular due to the computational complexity, see the introduction and references for details. The data format is fasta fasta format. Paste in your data in the form below.

The number of maximum number of sequences is 15 and their maximum length is 250 nucleotides. The maximum size of the motif to be searched for is 70 nucleotides. For any usage and or publication of cite all the references listed below.

Submit sequences

Your email:
(if you wish to be notified when your job is done)

Stop after aligning the following number sequences (max. 15):
Maximum motif size in nucleotides (max. 70):
Number of best alignments for greedy algorithm (max. 20):
Max window difference when comparing sequences (max. 8):

References
For usage of FOLDALIGN, please cite:

Finding the most significant common sequence and structure motifs in a set of RNA sequences. J. Gorodkin, L. J. Heyer and G. D. Stormo. Nucleic Acids Research, Vol. 25, no. 18 pp 3724-3732, 1997.
Abstract paper.ps.gz

Finding Common Sequence and Structure Motifs in a set of RNA Sequences.. J. Gorodkin, L. J. Heyer, and G. D. Stormo. ISMB 5;120-123, 1997.
Abstract paper.ps.gz

Comments, questions, etc., email foldalign@bioinf.au.dk

Last updated July 18th, 2001 by Jan Gorodkin