Anchored multiple alignment with DIALIGN [job submission]

This is a web server for multiple alignment of protein and nucleic acid sequences using DIALIGN with (optional) user-defined anchor points. A detailed online manual explains all features of the program. If you use our software for your research work, we kindly ask you to cite Morgenstern et al. (2006), Algorithms for Molecular Biology 1,6.

Please note that the present server is designed for protein and nucleotide sequences of moderate length, i.e. up to a few kb. For alignment of larger genomic sequences, we offer a specialized web server using the integrated CHAOS/DIALIGN software described by Brudno et al. (2003), BMC Bioinformatics 4,66

Submit your sequences:

Please upload your file in multiple FastA format

Sequence type Threshold fast_alignment

Your email address (optional)

Optional anchor points:

If you want to upload your anchor points, please use a file in this format (recommended for large sets of anchor points)

Alternatively, if you have only a few anchor points, you can put them into the table below.

first sequence second sequence start position in first sequence start position in second sequence length of anchor

Note that each anchor point corresponds to a pair of equal-length segments that are to be aligned. So an anchor point is characterized by two sequences, by the start positions of the segments and by the segment length. In addition, each anchor point needs a score that determines its priority in case of conflicting anchor points. If you enter anchor points by filling the above table, no scores for anchor points are required. Instead, proposed anchor points are prioritized by the order in which you input them.