Using Multiple Sequence Format (MSF) Files

You can combine multiple sequences in a single file, called a Multiple Sequence Format (MSF) file. MSF files include not only the sequence name but also the sequence itself, which is usually aligned with the other sequences in the file. You can specify a single sequence within an MSF file, a subset of sequences, or all sequences. Like other sequences, those in an MSF file can be used with other Wisconsin Package programs.

The following illustration shows an MSF file created with PileUp.

Figure 8

You may find the following components in an MSF file:

• File Type. (optional) Begins with the line (all uppercase) !!NA_MULTIPLE_ALIGNMENT 1.0 for nucleic acid sequences or !!AA_MULTIPLE_ALIGNMENT 1.0 for amino acid sequences. SeqLab uses the file type to improve performance when loading files. Do not edit or delete the file type. If present, it must appear on the first line of the file.

  　

• Description. (optional) Contains informative text describing what is in the file. You can add this information to the top of the MSF file using a text editor.

  　

• Dividing Line. (required) Must include the following attributes:
  
  MSF. Displays the number of bases or residues in the multiple sequence alignment.
  
  Checksum. Displays an integer value that characterizes the contents of the file.
  
  Two periods (..). Acts as a divider between the descriptive information and the following sequence information.

  　

• Name/Weight. (required) Must include the name of each sequence included in the alignment, as well as its length and checksum (both non-editable) and weight (editable).
  
  Note that the checksum of the individual sequences is important as a safety measure to ensure that you do not change the sequence data inadvertently. If this has happened, you will not be able to use the sequence(s) within the MSF file. You then can use the Reformat program to reformat the sequences and create a new checksum to reflect the file's edited contents.

  　

• Separating Line. (required) Must include two slashes (//) to divide the name/weight information from the sequence alignment.

  　

• Multiple Sequence Alignment. (required) Must include each sequence named in the above Name/Weight lines. This alignment allows you to view the relationship among sequences.

  　

Programs That Create MSF Files

To create an RSF file:

Choose from the following.

• SeqLab. You can export files to MSF from within the Editor of the graphical user interface to the Wisconsin Package. For more information, see "Exporting Sequences to MSF, GenBank, or GDE File Format" in Chapter 2, Editing Sequences and Alignments of the SeqLab Guide.

  　

• Wisconsin Package programs. The Wisconsin Package programs and their parameters (if necessary) that create MSF files are listed below.

  Program	Parameter (if necessary)
  LineUp	-MSF
  PileUp
  PrettyBox
  ProfileGap	-MSF
  ProfileSegments	-MSF
  Reformat	-MSF

Note: If you use % reformat -MSF to create an MSF file, it does not align the sequences.

Editing MSF Files

To edit an MSF file:

Use LineUp. For more information, see LineUp in the Program Manual.

You also can use a text editor to modify an MSF file. If you do so, however, the file's checksum changes, and Wisconsin Package programs will not recognize the file. Therefore, if you use a text editor to modify an MSF file, you must use the Reformat program with the -MSF parameter to rewrite it into GCG format.

Specifying MSF Sequences

To specify a single sequence, a subset of sequences, or all sequences within an MSF file:

Choose from the following.

• Single Sequence. To specify a single sequence within an MSF file, type the name of the MSF file and extension followed by the name of a sequence in curly brackets, for example, picorna.msf{cb3}.

  　

• Multiple Sequences. To specify a subset of sequences or all sequences within an MSF file, type the name of the MSF file and extension followed by a file specification and/or asterisk (*) wildcard in curly brackets. For example, picorna.msf{pl*} specifies all sequences in picorna.msf beginning with "pl", whereas picorna.msf{*} specifies every sequence in picorna.msf.

  　

  Note: You cannot use wildcards to name an MSF filename (that is, you cannot specify pic*.msf). You can use wildcards only between the curly brackets { }. Also, an MSF sequence specification must contain a sequence name or wildcard within the curly brackets. The MSF filename alone is not enough.

TIP - One way to specify a subset of sequences is to "comment out" those unwanted sequences within the MSF file. If you comment out sequences instead of deleting them, you can use them at a later time.

To comment out sequences:

1. Open the MSF file in the text editor of your choice and find the sequences you do not want to use in the Name/Weight area toward the top of the file.

   　

2. Type an exclamation point (!) in front of the "Name:" of each sequence you do not want. For example
   

   Figure 9

   　

   　

3. Save the file and exit the text editor.

   　

4. In response to a program prompt, type the MSF filename and extension followed by an asterisk (*) wildcard in curly brackets, for example picorna.msf{*}. The program will use only those sequences which are not commented out.