STRAP: Alignment of Protein structures and sequences

==> Visit the home page of the STRAP-application to get started.

For Life Scientists

Get the newest Bioinformatics methods to your desk. Analyzing and comparing homologous proteins. The Java program STRAP has the following features:

• Using 12 different sequence alignment methods.
• 3D structure superposition using the method CE/CL by Ilya N. Shindyalov and Philip E. Bourneto to superimpose two given protein backbones.
• multiple structure alignment using CE/CL
• Translation of DNA into amino acid sequence.
• Combining sequence alignments with 3D-structure visualization using Pymol by Warren Delano and Jmol. Picking residues in 3D to highlight them in the multiple alignment and vice-versa mark aligned residues in the 3D-view.
• One third of all proteins are transmembrane proteins. Highlighting TM-helical regions using more then 10 different prediction methods.
• Fetching data from sequence and structure databases.
• For most proteins now 3D-model is available. For those proteins a secondary structure prediction is valuable.
• Producing high quality images (PDF) of your results.
• Marking mutations and SNPs in 3D structures.

==> Visit the home page of the STRAP-toolbox.

For Bioinformaticians

Using the comprehensive STRAP API for self designed programs and scripts. Performing large scale analyses of protein structures and sequences in programs and scripts without GUI. Optimal toolkit for students of Bioinformatics.

Features

• Class names and methods are intuitive and the toolbox is easy to use.
• All utilities are explained with one example
• Combination with the BioJava toolkit is possible.
• Java classes developed with STRAP-Toolbox can be used as plugins for STRAP. STRAP utilizes a novel class hotswap technology which facilitates prototyping and parameterization of Bioinformatics algorithms. Program changes take effect without restarting the program.
• The API is optimized for speed. For example the PDB-parser reads 40 protein chains per sec on a 2.4GHz Pentium.
• Many different sequence alignment methods are accessible with one uniform interface. The global sequence alignment programs are: Align-m by Ivo Van Walle, ClustalW, Dialign 2 by Burkhard Morgenstern, Dialign T by Amarendran R. Subramanian, Mafft by Kazutaka Katoh, Muscleby Robert C Edgar, Neobio by Sergio.Carvalho, Probcons by Mahathi Mahabhashyam and T-Coffee by Cedric Notredame. Local alignment programs are JAligner by Ahmed Moustafa and Mafft by Kazutaka Katoh.