PACKAGE:charite.christo.strap. This tutorial takes about 40 min and explains the basics of STRAP. The quality of the text can be improved by typing CTRL-* (asterisk) at the expense of speed. The tutorial contains menu items that are located in menus of the menu-bar and in WIKI:Context_menus. As you press these menu-items the containing menu is indicated. Also consider to watch the Flash videos http://www.bioinformatics.org/strap/#DOCUMENTATION.

Printing

As you press CTRL+P this text appears in the Web-browser where it can be printed. Remember to give the text the key-board input focus by left-click. If not go the section "trouble-shooting" at the end of this text where configuration of the Web-browser is explained.

Computer-Basics

Before you continue with STRAP, it is recommended that you are familiar with a few elementary concepts of graphical computer systems. They are common to all Desktop systems like Windows, Macintosh, KDE and Gnome. Macintosh differs slightly from other systems. The best is you take your text processor and your file browser (On Windows this is the Explorer.) and check the following:

Obtaining example proteins for this tutorial

In this tutorial we compare three subunits of the core of the WIKI:Proteasome. The protein files are downloaded into the project directory and appear in the Sequence alignment pane below. BUTTON:Tutorials#bExampleFiles("INTRO")!

Aligning some sequences

The button BUTTON:DialogAlign! opens the WIKI:Sequence_alignment dialog. First you need to select an alignment method and the proteins that should be aligned. Take COMBO:MultipleAlignerClustalW, which is the most popular sequence alignment program. After starting computation by pressing the button LABEL:ChButton#BUTTON_GO a result panel with the alignment preview appears. Generally, dialogs in STRAP may have several result tabs. Return to the main tab of the dialog. Start the computation again with a different set of proteins or with different WIKI:Gap_penalty ( tool-button ICON:IC_CONTROLPANEL). Each computation brings a new result tab with an alignment preview.

Selecting more than one protein: CTRL+left-click toggles selection and SHIFT+left-click selects a range.

Evaluating the alignment

When the alignment process is finished a preview with the result appears. You can inspect the result and accept it by pressing LABEL:DialogAlignResult#BUT_LAB_Apply. By accepting the alignment the alignment gaps are conferred to the working alignment in the main alignment pane. Would you consider the sequence alignment to be accurate? Let's evaluate the alignment using additional information from WIKI:protein_structure. In the tool-bar the shading style JCOMPONENT:StrapView#choiceShading()! should be set to "secondary structure". Please drag the slider JCOMPONENT:StrapView#sliderSimilarity()! below the alignment panel so that the scroll-bar is shaded according to the secondary structure (Helices red and sheets yellow). Sequence insertions and deletions during evolution usually avoid the middle of helices and beta sheets. Apparently, this is not the case her since gaps are found in the middle of helices.

The active site residues Gly 129

The β-subunits are catalytically active whereas the α-subunits are not. Now we regard the active site residues of the sequences hs_... and b1_... The active site has a Gly-Ser-Gly-motif. Go with the cursor to the pdb residue number 129: in hs_... and b1_... . In the alignment header the residue index, and the residue PDB number, and the alignment column is written. PDB numbers are recorded in the PDB-file (see the PDB listing below) whereas residue indices count from 1 to the total number of residues. To distinguish residue indices and PDB numbers the latter are followed by a colon and the WIKI:peptide chain letter. Move the cursor to the PDB residue number 129:. You may use the cursor keys but a convenient way is to type "129n". You can also search for the text string "GSG" to quickly find the position BUTTON:DialogHighlightPattern!. Comparing hs_... and b1_... you see that the active site sequence motif Gly-Ser-Gly is not well aligned with sequence based methods.
Conclusion: Computations based on amino acid sequence alone fail for remote homologs

Structural Alignment

Next we perform a WIKI:Structural_alignment using 3D-structure. We compute the alignment with COMBO:ClustalW_3D which is a combination of WIKI:ClustalW and a 3D superposition program. It can perform alignments for structures and sequences.
Result: The active site residues are aligned well.

Editing the Alignment

Click in the alignment to get a text-cursor. Cursor navigation and text editing works like in MS-Word with the difference that only white space can be inserted or deleted, but the amino acids cannot be changed. The row headers with the protein names can be dragged up and down to change the order of proteins. Dragging them outside the application frame results in a copy of the protein file on the desktop (see WIKI:Drag_and_drop). right-clicking a protein name brings up the context-menu. Hovering with the mouse over the protein icon brings up a tool-tip. For more info see DIALOG:StrapKeyStroke.
Exercise:
  1. Insert and delete gaps using the SPACE, DELETE and BACKSPACE keys.
  2. Change two proteins simultaneously by selecting the two proteins".
  3. Insert exactly 13 white spaces by typing "1" "3" "space-bar".
  4. Change the order of the proteins.
  5. Drag a protein to the desktop.

Cut-and-Paste and Drag-and-Drop (D&D)

As an example for a 3D-structure file create a WIKI:Plain_text file with the following PDB-text (WIKI:Protein_Data_Bank) in a text editor like WIKI:Wordpad. Use CTRL+C and CTRL+V to copy the text into the text program (see WIKI:Cut_paste).

Drag-and-Drop text selection: This does not work in WIKI:Notepad but in WIKI:Wordpad. Now select the entire text in the text editor. The drag the selection with the mouse into the STRAP application.

Drag-and-Drop a file: Next, D&D of files will be demonstrated: Save the file as plain text and not as MS-Word- or HTML- or RTF-document and avoid white space in the file name. Then drag the file with the mouse to the STRAP application (see WIKI:Drag_and_drop).
  ATOM   7121  N   TYR E   8     -48.777  48.007  60.590  1.00 93.66
  ATOM   7122  CA  TYR E   8     -48.065  47.524  59.366  1.00 94.20
  ATOM   7123  C   TYR E   8     -46.621  48.045  59.286  1.00 93.97
  ATOM   7124  O   TYR E   8     -46.388  49.225  58.982  1.00 94.01
  ATOM   7125  CB  TYR E   8     -48.843  47.939  58.113  1.00 93.81
  ATOM   7126  N   ASP E   9     -45.660  47.159  59.562  1.00 93.07
  ATOM   7127  CA  ASP E   9     -44.236  47.509  59.520  1.00 91.34
  ATOM   7128  C   ASP E   9     -43.460  46.529  58.631  1.00 89.29
  ATOM   7129  O   ASP E   9     -43.402  45.326  58.893  1.00 88.80
  ATOM   7130  CB  ASP E   9     -43.636  47.510  60.929  1.00 92.28
  ATOM   7131  CG  ASP E   9     -42.367  48.335  61.017  1.00 93.09
  ATOM   7132  OD1 ASP E   9     -42.464  49.577  60.879  1.00 94.24
  ATOM   7133  OD2 ASP E   9     -41.280  47.746  61.214  1.00 91.48
  ATOM   7134  N   ARG E  10     -42.847  47.067  57.586  1.00 86.76
  ATOM   7135  CA  ARG E  10     -42.106  46.269  56.623  1.00 83.63
  ATOM   7136  C   ARG E  10     -40.747  46.902  56.347  1.00 81.14
  ATOM   7137  O   ARG E  10     -40.468  48.005  56.816  1.00 81.28
  ATOM   7138  CB  ARG E  10     -42.914  46.218  55.333  1.00 84.67
  ATOM   7139  CG  ARG E  10     -43.446  47.597  54.948  1.00 86.88
  ATOM   7140  CD  ARG E  10     -44.011  47.619  53.547  1.00 90.08
  ATOM   7141  NE  ARG E  10     -45.381  47.120  53.465  1.00 92.28
  ATOM   7142  CZ  ARG E  10     -46.457  47.899  53.403  1.00 93.17
  ATOM   7143  NH1 ARG E  10     -46.327  49.224  53.414  1.00 92.66
  ATOM   7144  NH2 ARG E  10     -47.664  47.352  53.311  1.00 93.60
  ATOM   7145  N   GLY E  11     -39.911  46.213  55.573  1.00 77.52
  ATOM   7146  CA  GLY E  11     -38.601  46.755  55.240  1.00 72.46
  ATOM   7147  C   GLY E  11     -38.700  47.944  54.298  1.00 69.15
  ATOM   7148  O   GLY E  11     -39.699  48.105  53.591  1.00 67.56
D&D makes loading of proteins much easier. Without the convenience of D&D the user would need the dialogs ITEM:DialogNewProtein! or ITEM:MainDialogProjectFiles!.

D&D is a very important concept in STRAP. Please see the D&D-Tutorial and http://3d-alignment.eu/dragProteinLink.html.

Several alignments simultaneously

Sometimes it is necessary, to probe a different alignment strategy or to compare the loaded proteins with other protein files without affecting the working alignment. In this situation it is necessary, to open another independent STRAP-Window with the same or a different project directory. Data exchange between the two alignment panels works simply by WIKI:Drag_and_drop. Select all proteins in one STRAP Window. Use SHIFT for selecting a range of proteins. Start a second STRAP session. Then drag the proteins to the other STRAP Window.

Altering the amino acid sequence

Protein files can be changed with a text editor such as WIKI:Microsoft_Word, WIKI:Wordpad, WIKI:VI or WIKI:Emacs. As soon as the changes to the protein file are saved STRAP will reload the protein. The menu item BUTTON:ProteinPopup#docuSelectedEditProtein()! is found in the WIKI:Context_menu (right-click a protein label). Go to section "Trouble-shooting" if no suitable text-editor is opened.

Text searching

CTRL+F opens the text search dialog. For example to search for a menu item open BUTTON:StrapAlign#button(CMD_ALL_MENUS)! or BUTTON:StrapAlign#button(CMD_ALL_POPUP)!. Click into the text to set the input focus. Enter a query into one of the text search fields.

Trouble-shooting

Plain text format: Some text-editors like the default editor on Macintosh create a document in WIKI:Rich_Text_Format (RTF). Also office programs usually save text in special formats but can be directed to produce plain text. These special WIKI:Document_file_formats are not suitable for STRAP and only WIKI:Plain_text is supported.

Starting programs like Web-browser from STRAP: Starting an external program from STRAP such as a Web browser may not work properly. To identify problems the log-panel of this process can be opened: Hold CTRL i while the mouse click is performed. For example click the Google URL GOOGLE{strap proteins} holding the CTRL key. With the control-panel you can watch and alter the shell command and read the standard output of the programs. The standard programs like text editor and Web-browser can be specied in the menu "Preferences": BUTTON:Customize#newButtonAll("A")!.

Embedded Bioinformatics programs:

ClustalW and TM-Align are ready to use because pre-compiled WIKI:Executables are provided for ClustalW and TM-Align for Windows, Mac and Linux386. Other programs are installed from source code to ensure that the programs are working on any operation system and are optimized for the particular processor type.