STRAP A user-friendly Java program that aligns proteins by sequence and 3D-structure
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protein align Biology align protein mRNA sequence protein annotation

STRAP Description

A user-friendly Java program that aligns proteins by sequence and 3D-structure STRAP is a cross-platform program that supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, 3D-structure and genomic- and mRNA-sequence, secondary structure and residue annotation.The alignment can be exported and modified in MS-Word or other text processors The included tutorial will teach the use of STRAP in as little as one hour. The scriptability and extendability make STRAP a very powerful tool for even the most advanced users. Here are some key features of "STRAP": · Computation of sequence alignments · Computation of WIKI: 3D-superpositions (Example output) and structure based multiple alignments of proteins with PUBMED:TM-align or CE or Gangsta+ 3D-superposition. Combined sequence-structure alignments. · 3D-visualization using WIKI:Pymol or WIKI:Jmol or Rasmol and VMD. In preparation: yasara Highlighting mutations, WIKI:SNPs, WIKI:exon-intron boundaries or regions with high sequence conservation in 3D. Instant cross-selection between 3D objects, sequences and alignments · WIKI:Blast search including "Blast Alert" · Prediction:WIKI:Transmembrane helices, WIKI:Secondary Structures and WIKI:Coiled-Coil · Translation of nucleotide sequences to amino acid sequences. Output of amino acid alignments as nucleotide alignments. · Protein file formats: WIKI:Swissprot, WIKI:PDB, WIKI:Fasta, MSF, BIOWIKI:Stockholm, WIKI:Clustalw, WIKI:Nexus, HSSP WIKI:Genbank, EMBL · Phylogenetic trees with ATV, WIKI:Jalview and GeneBee · Residue annotations and nucleotide annotations Highlighting WIKI:regular expressions (i.e. Prosite-Patterns) using WIKI: Incremental search and WIKI:sequence features from WIKI:DAS servers: Aiding tricky sequence alignments due to low sequence similarity by: · 3D-superposition of C-alpha atoms using CE and TM-align to highlight spatial equivalent residues · Dotplot · Intermediate Sequences · Mixed sequence alignments and protein structure alignments · WIKI:Plugins are extensions for STRAP from third-party developers. Requirements: · Java · compilers for Objective-C and Fortran

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