STRAP: editor for STRuctural Alignments of Proteins

STRAP is a comfortable and extensible tool for the generation and refinemen t of multiple alignments of protein sequences. Various sequence ordered inp ut file formats are supported. These are the SwissProt-, GenBank-, EMBL-, D SSP- PDB-, MSF-, and plain ASCII text format. The special feature of STRAP is the simple visualization of spatial distances of C-alpha-atoms within th e alignment. Thus structural information can easily be incorporated into th e sequence alignment and can guide the alignment process in cases of low se quence similarities. further STRAP is able to manage huge alignments compri sing a lot of sequences. The protein viewers and modeling programs INSIGHT, RASMOL and WEBMOL are embedded into STRAP. STRAP is written in Java. The w ell-documented source code can be adapted easily to special requirements. S TRAP may become the basis for complex alignment tools in the future.