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Bioinformatics Vol. 17 no. 4 2001
Pages 377-378
© 2001 Oxford University Press

Applications Note

STRAP: editor for STRuctural Alignments of Proteins

Christoph Gille * and Cornelius Frömmel

Institute of Biochemistry, Charité, Medical Faculty of the Humboldt University, Monbijoustraße 2a, 10117 Berlin, Germany

Received on May 9, 2000 ; revised on October 24, 2000 ; accepted on November 22, 2000

Summary: STRAP is a comfortable and extensible tool for the generation and refinement of multiple alignments of protein sequences. Various sequence ordered input file formats are supported. These are the SwissProt-,GenBank-, EMBL-, DSSP- PDB-, MSF-, and plain ASCII text format. The special feature of STRAP is the simple visualization of spatial distances of -atoms within the alignment. Thus structural information can easily be incorporated into the sequence alignment and can guide the alignment process in cases of low sequence similarities. Further STRAP is able to manage huge alignments comprising a lot of sequences. The protein viewers and modeling programs INSIGHT, RASMOL and WEBMOL are embedded into STRAP. STRAP is written in Java. The well-documented source code can be adapted easily to special requirements. STRAP may become the basis for complex alignment tools in the future.

Availability: The tool is available to academic institutions at http://www.charite.de/bioinf. The source code can be requested via e-mail.

Contact: christoph.gille{at}charite.de

* To whom correspondence should be addressed.


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