University of Göttingen | Faculty of Biology | Inst. of Microbiology and Genetics | Dep. of Bioinformatics


This is a WWW server for multiple alignment of protein sequences using DIALIGN with secondary structure prediction.

The secondary structure input is computed by the PSIPRED V2 software described in Jones DT (1999), J. Mol. Biol. 292: 195-202.

The structure prediction is used to increase or decrease the weight of a fragment according to the amount of similar secondary structure shared by the segments composing the fragment. In this way, the order into which the fragments are included to construct the multiple alignment can be different from the one given by the DIALIGN weight function. This can lead to the inclusion of structurally relevant segments having an otherwise low overall primary sequence similarity.

A tutorial explains the features of the secondary structure output. Click here to upload into the submission form the sample data corresponding to the running example featured in the tutorial.

Submission form

Note that the present server is designed only for protein sequences of moderate length, i.e. up to a few kb. For the alignment of larger protein sequences for which the secondary structure prediction fails to produce any output, or for genomic sequences, please use other versions of Dialign.