CHAOS + DIALIGN [job submission]

Pair-wise and multiple alignment of genomic sequences with CHAOS and DIALIGN

By Mike Brudno and Burkhard Morgenstern

This service calculates pair-wise and multiple alignments of genomic sequences using CHAOS and DIALIGN as described in If you use our software for your research, please cite this article. CHAOS is used to rapidly identify strong sequence similarities that serve as anchor points to speed-up the DIALIGN alignment procedure. Details about the CHAOS/DIALIGN procedure are available here. In addition, our web page now offers the interactive multi-alignment visualisation tool ABC by Greg Cooper et al. (2004), BMC Bioinformatics 2004, 5:192, see below.

Program Input:

Upload sequences in multiple FASTA format
(as a TEXT file, not MS-Word, not RTF!)

Your email address

Program Output:

Our server creates four different output files from your input sequence set. The full alignment is returned in DIALIGN format. In addition, a list of fragments, i.e. gap-free segment pairs created by DIALIGN is returned, as well as anchor points created by CHAOS and the full alignment in FASTA format.

You will receive an email containing the URL of the chosen output files. These files can be accessed during the next 5 days. For small input data sets, the output alignment is shown on the screen - either in DIALIGN format or using the visualisation tool ABC if you check this option.

Alignment Visualisation using ABC:

If you have activated Java in your browser, we offer the multi-alignment visualisation tool ABC for interactive graphical representation of the program output.
Please note that ABC requires sequences that are at least 25 residues long.

Use ABC, I have Java activated in my browser.