Written by Jamie Hatfield     01/2002

Contents

Description

Interface

• FPC Directory

  This is the directory that your FPC files are located in. FSD also expects the sequences that you wish to digest to be in a directory under your FPC directory.
  Default: <Current directory>

• Sequence Directory

  This is the directory under your FPC directory that the sequence files are located in. You can choose from a list of all directories.
  Default: fsd (if available)

• Sequence File

  You can choose from a list of sequence files in the Sequence Directory if you would like to digest a single file, or you can just digest all files by choosing ALL_FILES.
  Default: ALL_FILES

• Restriction Digest

  This is a list of restriction digests. You can choose from the ones in the list and the actual enzyme will be displayed to the right, or you can specify your own by choosing OTHER and typing the enzyme in the box to the right. The period (.) specifies the cut location.
  Default: hindiii

• Standard File

  This specifies where FSD should find the standard file used by Image. This is the file that gives FSD the information necessary for it to translate sizes to bands.

• Subclone

  Subcloning is used so that the clones generated from a sequence are not too long. Checking this box will cause FSD to split the original sequence up into sub-sequences before performing the simulated digest. The size of the sub-sequences is specified in the Size box, and the percent overlap is specified in the % Overlap box. This is necessary when the sequence is much larger than the clone size. Otherwise, the simulated digest clones will not automatically assemble with real data.
  Default: <checked>; size = 180000, % Overlap = 80
  
  These default settings would cause a sequence to be divided up as follows:
  

  bp      1 - 180,000: first clone
  bp 36,001 - 216,000: second clone
  etc...
  

  The exception to this is if your sequence length is between 180k and 216k in size. In this case, it wouldn't make sense to make a second clone, since there really isn't enough to make the two clones substantially different (FPC would just bury the second one in the first one). In this case, the first clone would contain the entire sequence. Similarlly, if there isn't enough overlap to make a good sized third clone, the leftover will just be added into the second clone.
  
  The .bands and .sizes files have the following format: xxxxsd.bands and xxxxsd.sizes. The "xxxx" portion is just the original sequence filename from the Sequence Directory. The generated clones have a similar naming: xxxxsd01 will be the first clone generated from a sequence, followed by xxxxsd02, etc.
  

• Min/Max Fragment Size

  This setting keeps the simulated digest in line with a lab digest. In a actual lab digest, the fragments that are too small will "run" off the end of the gel, and thus not be recorded. These fragments are below the Minimum Fragment Size. Also, the fragments that are too large will not move far enough out of the well at the top of the gel to be distinguished from each other or the well. These fragments are above the Maximum Fragment Size. Testing showed that the default values most closely represent actual lab conditions. They may need to be altered for your particular needs.
  Default: 1000, 200000 (specified in bp's)

  
  There are also three buttons along the bottom:
  
  
• Write Defaults

  Writes the current settings to a file named .simulate in the directory specified by FPC Directory. These will be read in automatically the next time FSD is started in the specified FPC Directory.

• Digest

  Perform the simulated digest.

• Close

  Exit the program.

  
  
  

  Batch Mode

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  You can run FSD in batch mode by specifying "b" as the first option. Other arguments can be included to set default values as descirbed in Command line options below. No user interface will be brought up, so this can be ran from a script. It will simply do the digest with the specified options.
  
  

  Command line options

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  This is most useful for batch mode, but you may also use it to override defaults or settings saved in .simulate by "Write Defaults".

                  fsd [b] [<options>]
  
          b specifies batch mode (no user interface)
          options:
                  f <fpcdir>
                          Set the FPC directory to <fpcdir>
                  d <seqdir>
                          Set the sequence directory to <seqdir>
                  s <seqfile>
                          Set the sequence file to <seqfile>
                  e <enzyme>
                          Set the Restriction Digest to <enzyme>
                  n <stdfile>
                          Set the standard file to <stdfile>
                  c <size> <overlap>
                          Subclone sequence into <size> bp
                          clones with <overlap>% of overlap
                  m <minSize>
                          Minimum fragment size = <minSize>
                  x <maxSize>
                          Maximum fragment size = <maxSize>