Introduction
[Menu-bar>Tutorials] Did you ever wish to compare protein sequences or to identify 3D
structures of proteins that are similar to your protein?
Are you interested in remote phylogenetic relationships to discuss the function of a protein?
Do you want to take advantage of the experiences of the Bioinformatics community to
explore your proteins?
Making sequence alignments of related protein sequences is a common task in biology.
It reveals regions which are highly conserved and are functionally important.
Automatic approaches alone are often not fully satisfactory and manual
refinement is necessary in most cases particularly when the sequences
are very dissimilar.
STRAP is a
comfortable and comprehensive tool to edit multiple protein sequence
alignments.
A wide range of functions related to protein sequences and
protein structures are accessible with an intuitive graphical
interface.
STRAP is tightly integrated into your desktop environment supporting
and and spell check.
is available for proteins, nucleotide structures and hetero structures.
for proteins, annotations and files are triggered by right mouse click.
The program appears to be complicated in the beginning.
With the help of the integrated tutorials you will learn how to
apply the currently available methods to compare proteins sequences
and structures.
The key features are:
- Visualization and manipulation of sequence alignments (up to 1000 sequences)
- Automatic computation of multiple sequence alignments by Clustalw (Fukami-Kobayashi & Saito, 2002) and many other algorithms.
It can combine amino acid sequences alignments and protein structure alignments.
- Loading protein files from public databases
- BLAST searches
- Structure prediction
- 3D-visualization using either PyMol, Rasmol, VMD, JMol or ProteinWorkshop
- 3D-superposition of C-alpha atoms
- Dot-plots
- High quality PDF output by LaTeX/TeXshade
- Project safety by included backup system
- Translation of nucleotide sequences to amino acid sequences
- Residue selections
- Highlighting ion
- Residues adjacent to ligands
- Text annotations of residues including:
- Notes
- Hyperlinks
- 3D-rendering commands
-
Optimized performance
- Reduced memory consumption
- Extremely fast loading of proteins
- Cache for computed results such as alignments and Blast-results
What it cannot do:
- Docking
- Gene structure, promotor analysis
- Structure modelling
- Molecular dynamics
- Gene expression
- RNA-3D-structure
Online documentation
Help
Java is available in advanced user mode.
Frequently occurring buttons
Setting of program parameters such as 
Customization such as addresses for protein files
Detach from main window and display in a separate window
Show/hide
Setting color
Closing a view usually without loss of data
Discard
Report bugs to:
christoph.gille(at)charite.de