(C) Instructions for running mfg

Size: px

Start display at page:

Download "(C) Instructions for running mfg"

Lester Perkins
6 years ago
Views:

1 (C) Instructions for running mfg Before you start you should add the DINAMelt website to your favorites for future use. 1.) Copy the sequence of interest to be folded and save to the clipboard. Mfold may not analyze an input sequence that is more than 500 bases. Be sure to include the equivalent of at least one window size of bases before your sequence of interest and twice that many following your sequence of interest (See example below for general rules). Save the edited sequence in a word file to be used with mfg in the future. Example: Number of Bases Before = Window Size Length 40 Bases Sequence of interest (40 nts) gattccacac ccccgcccgg cacccgcgtc cgcgccatgg ccatctacaa gcagtcacag cacatgacgg aggttgtgag gcgctgcccc caccatgagc gctgctcaga tagcgatggt gagcagctgg ggctggagag acgacagggc tggttgccca gggtccccag gcctctgatt Number of Bases After = 2X Window Length 80 Bases 2.) Open the mfg program by double clicking on the shortcut to mfg. Click on the 1 st icon (a). Once selected, the [Freeware] - Input Sequence window will appear. a b c 3 Icons a- input original sequence b- generate subsequences c- analyze ct file from mfold 1

3.) Right click anywhere inside the Enter Sequence box and paste in your sequence of interest. Enter a Sequence Name (optional) if desired and select OK. 4.

This is generally too small to provide a complete analysis of a sequence. Suggested frame lengths are between 40nts 80nts. Click on Generate Subsequences (b).

2 3.) Right click anywhere inside the Enter Sequence box and paste in your sequence of interest. Enter a Sequence Name (optional) if desired and select OK. 4.) Select the 2 nd icon and a [Freeware] - Generate Subsequences window will appear. Specify the frame length (a) (window size). Note that the default Frame Length is 30nt. This is generally too small to provide a complete analysis of a sequence. Suggested frame lengths are between 40nts 80nts. Click on Generate Subsequences (b). The subsequences should appear in the window (c). Select Copy to Clipboard (d) and then close the [Freeware] -Generated Subsequence window and minimize the [Freeware] - mfg application. (Note: currently the Launch Quickfold Server operations does not work.) a b c d 2

5.) The copied subsequences can now be used to interface with mfold. Go to Zucker s DINAMelt server at: http://www.bioinfo.rpi.edu/applications/hybrid/quikfold.php.

3 5.) The copied subsequences can now be used to interface with mfold. Go to Zucker s DINAMelt server at: Paste subsequences into the Sequences box (a). Enter a name for your job in the box provided (b) or mfold may not run your sequence. Click on the Submit button at the bottom of the screen (c). (The default experimental conditions can be adjusted to your specifications). b a c 3

6.) When the DINAMelt Server has finished folding the subsequences, the results will appear as seen below.

Under the Results heading you will see All foldings: ct file, Mac ct, RNAML, PDF. Right click on ct file (in red).

Save the file in your mfg folder (located in my computer/ Local disk (C:)/ mfg) with a unique name.

) Open your ct file by selecting the 3 rd icon (analyze CT file) and the Open window will appear.

4 6.) When the DINAMelt Server has finished folding the subsequences, the results will appear as seen below. (Note: if the screen remains blank hit the refresh icon to update the results). Under the Results heading you will see All foldings: ct file, Mac ct, RNAML, PDF. Right click on ct file (in red). Select Save Target As and a Save As window will appear. Save the file in your mfg folder (located in my computer/ Local disk (C:)/ mfg) with a unique name. Close the download box and the web page and open your minimized [Freeware] mfg application window. 7.) Open your ct file by selecting the 3 rd icon (analyze CT file) and the Open window will appear. Locate and double click on your newly saved CT file to be analyzed by mfg. A black Mfe.exe window will appear as the run is being processed. This window closes automatically when the run is finished and the analyzed data will appear in the mfg window. 4

8.) The mfg program will now display the output for your analyzed sequence. Note that the first sequences generated with less than a full window size of bases (i.e. 1-to-39) are displayed, but should be ignored.

5 8.) The mfg program will now display the output for your analyzed sequence. Note that the first sequences generated with less than a full window size of bases (i.e. 1-to-39) are displayed, but should be ignored. Segments of sequence can be seen in the Current Sequence window with the specified folding window highlighted. A table displaying the information for each base appears below the sequence. The information for any base can now be viewed by highlighting the base of interest. To view the most stable secondary structure in which the selected base is unpaired, select a fold from the MaxE Sequences box to the right of the table. (Note: there may be more than one fold with the same energy). The secondary structure will appear in the box to the right of the list, with the selected base colored red. The eight fields of the table are defined below. Table Column Headings Nt- mfg assigned nucleotide number based on its location in the given sequence. Base- The base at the nt position. Folds- Number of folds used in the folding Frame (Window size), must be at least equal to the frame size to be valid. Unpaired- Total folds in which this base is unpaired (out of all folds analyzed). %Unp- Percent unpaired (unpaired folds / total folds). MaxE- Maximum-energy ( G) secondary structure in which this base is unpaired. FrUE- Mutability index (MI) product of % unpaired and - G. TSeq- Total number of subsequence(s) of maximum-energy fold. Selected base nt 48 5

6 9.) Note: The data in the table are displayed 5 to 3 from the lowest nt number to the highest nt number as a default. Images can be saved by taking a screen shot using the control+ print screen function (on keyboard) and pasting to the Paint or PowerPoint programs. 10.) If mfg crashes or you want to view an old run, select the 1st icon (input sequence) and paste the original sequence folded into the input sequence window, then select the 3rd icon (analyze CT file) and double click on the file you wish to view. The run will be processed again and the data and structures can be viewed. 6

Instructions for Importing mfg Data into Excel 1.) The data can now be imported into Microsoft Excel.

Locate your mfg folder in the C drive (located in my computer/ Local disk (C:)/ mfg) and open it.

This should display a large number of new files in the window. Double click on the file named ~outct.ana.tmp.

7 Instructions for Importing mfg Data into Excel 1.) The data can now be imported into Microsoft Excel. Minimize the [Freeware] mfg application window and open Excel. Select File and Open. Locate your mfg folder in the C drive (located in my computer/ Local disk (C:)/ mfg) and open it. Change the Files of type: from All Microsoft Office Excel Files to All Files. This should display a large number of new files in the window. Double click on the file named ~outct.ana.tmp. The Text Import Wizard will open. In Step 1, choose Delimited and then click Next. In step 2, uncheck Tab and check Space. Finally, click Finish and your data will be imported. 7

2.) The newly created excel file will appear as follows. Delete The first eleven rows can be deleted.

If deleted, insert a row at the top in order to add headings for each column. The default headings are seen below.

Columns J and beyond contain more complex information not discussed in this tutorial and can be deleted. 3.

8 2.) The newly created excel file will appear as follows. Delete The first eleven rows can be deleted. They provide the date, time, file name, and column headings. If deleted, insert a row at the top in order to add headings for each column. The default headings are seen below. A-Blank (no data), B-NT, C-Base, D-Folds, E-Folds, F-Unpaired, G-% Unpaired, H- G, and I-MI. Columns J and beyond contain more complex information not discussed in this tutorial and can be deleted. 3.) Copy the data of interest to a new Excel file and save, or save the data directly once it has been imported into the Excel file. If saving directly be sure to change the Save as type: from Text (Tab delimited) to Microsoft Office Excel Workbook in order reopen the file with Excel in the future. 8

Budget Reports for All Users

Budget Reports for All Users Table of Contents: How to Open the MBI - Budgeting Cost Center & Rollup Report..2 How to Open the MBI - Budget Excel Format Cost Center & Rollup Report...7 How to open a TSV