MatGAT 2.0 Tutorial

Important:  During the very first start MatGAT will try to locate Excel. This operation may take a few seconds.

MatGAT consists of three tabbed panels: "Input Panel", "Results" and "Configuration" their detailed functions are explained below.

                                                                                                                         Figure 1. MatGAT at start up

• The screen shot above shows the input area of MatGAT
• Scoring Matrix pull down menu will be enabled when the "Protein" option is chosen.
• Use the "Browse" button to choose and load a file that contains protein/dna sequences

                                                                                                                              Figure 2. After "Browse" button has been clicked

• To load a file into MatGAT double click a file in the "Open" window, or chose a file and press the Open Button
  (This operation may take a few second (depending on your machine and size of file), because formatting is taking place)
   
• The "Copy" and "Paste" button have the same functionality as they do on other software
• Select the text and press Copy, to copy the text
• Select the pasting position and then press the "Paste" button
   
• Use the "Scoring Matrix" pull down menu to choose a scoring matrix for the alignment process (Protein Only)
• Edit the "First Gap" and "Extending Gap" fields to set the gap opening and gap extending penalty for the alignment process
• After you load a file and set the alignment parameters press the "Align" button to start the alignment process
• Press the "Clear" button to clear the input area and process another set of sequences

                                                                                                                         Figure 3. After "Align" button has been clicked

• When the alignment process is done the "Results" tab is shown

            The table

• For space saving purposes the naming is displayed only once in the first column
• The user can view/save individual alignments by double clicking in a table cell (upper triangle recommended)
• The upper triangle of the table displays the alignment  identity score
• The lower triangle of the table displays the alignment  similarity score
• For ease of use the upper and lower triangles are color coded.
  (The background and foreground color of the upper and lower triangle can be changed using the "Configuration" tab, see below)
  
  Example. The cell highlighted in red with value "33.9" shows the identity score of the alignment of 1^st row (i.e. 1^st sequence, C. jejuni) and
                 the 2^nd column (i.e. 2^nd sequence, Wheat)
  
                 The identity score of the alignment of C.jejuni and Wheat (should be in the upper triangle) can be found by firstly identifying the
                 the sequence which is higher in the first column, in this case C.jejuni, this is the row where the score will be located. To find the
                 column in which the score is located use the number next to the other sequence, in this case Wheat, which happens to be 2,
                 so identity score is located in the row named C.jejuni and the second column i.e. Identity score is "33.9".
  
                 The similarity score of the alignment of C.jejuni and Wheat (should be in the lower triangle) can be found by firstly identifying the
                 the sequence which is lower in the first column, in this case Wheat, this is the row where the score will be located. To find the
                 column in which the score is located use the number next to the other sequence, in this case C.jejuni, which happens to be 1,
                 so similarity score is located in the row named Wheat and the first column i.e. Similarity score is "50.5".
  
                Let's try another one. "Rice" (5)  vs "Tomato" (3)
                
                Following the directions above, the identity score should be located in the upper triangle, in the third row named "Tomato" and
                in the fifth column, therefore the identity score is "37.6". Similarly, the similarity score should be located in the lower triangle, in the
                fifth row named "Rice" and in the third column, therefore the similarity score is "57.0".

            The bottom bar

• The alignments can be exported into a text file for later processing in other statistical or spreadsheet tools (Excel, Jump and other tools)
• Use the "Column Delimiter" drop down menu to select a character to separate the columns when exporting the alignment table. Check the
  the program in which you are trying to import the table for delimiter characters in which that program is able to accept the data.
  MatGAT is able to delimit columns with "Tab" (Excel's default), "Space",  "Comma"  or "Semicolon".
• Use the "Export" button to save the alignment table into a file, with columns delimited with the character chosen in "Column Delimiter"
• If the "Excel" button is active, you can view the data in Excel with a single click of this button
• Use the "Print" button to print the alignment table
• You have the choice to see, similarity scores only, identity scores only or both, by checking or clearing the "Similarity" and "Identity" checkboxes (color coded to match the colors used in the table)
• The user can select alignments to be saved (up to 12), by double clicking on the cells (i.e. viewing the alignments) and then clicking the Save "Selected" button, .txt (plain text, will not show ok on Notepad, try WordPad or Word) and .rtf (rich text format, preferred/default) format.
• Or the user can choose to save all the alignments, to do this click on Save Alignments "All" button. This operation may take a few seconds or minutes to complete depending on the number of sequences their length and the computer you are using. This operation takes longer than the initial alignment which generates the alignment table.

                                                                                                                         Figure 4. The "Configuration" tabbed panel

• In this panel you can control:
  1.  The foreground/background color of the Similarity and Identity scores (i.e. lower and upper triangle of the alignment table)
  2.  The location of Excel.exe  (Microsoft Excel)

• To change a color firstly press the choose button next to the color you want to choose, then change the slider position until you see the desired color in the color view area,  click the default mouse button (for right/left handed the left/right button) to preview the color (a small square will appear in the position you clicked) the color box next to the "Choose" button you clicked will show the color that you just chose. To select this color click the other mouse button (for right/left handed the right/left button), the alignment table will be updated automatically, and the new colors will be used.
   
• To select another location for the Excel.exe file click the "Browse" button to look through your file system to locate Excel in case MatGAT was not able to find Excel or has found a version you do not want to use.
   
• Keep in mind that all configuration changes MUST be saved by clicking the "Save" button if you want to make these changes permanent (i.e. when MatGAT is executed again it uses the configurations you chose) 

Please email questions or suggestions about this page or this application to Ledion Bitincka at ledion@bitincka.com