The Reverse Primer

The example below shows how to find the reverse primer in a single step. The SmaI recognition sequence is ccc'ggg and the primer sequence is gaccatg'.

 Select operation
 X  1 Search
    2 List enzyme file
    3 Clear text
    4 Clear graphics
 ? Selection (1-4) (1) =
 Select input source
    1 All enzymes file
 X  2 Six cutter file
    3 Four cutter file
    4 Personal file
    5 Keyboard
 ? Selection (1-5) (2) =5
 Define search strings by typing a string name 
 followed by the string(s)
 ? Name=p
 ? String(s)=gaccatg'/ccc'ggg/
 ? Name=
 ? Search for all names (y/n) (y) = 
 Select results display mode
 X  1 Order results enzyme by enzyme
    2 Order results by position
    3 Show only infrequent cutters
    4 Show names above the sequence
 ? Selection (1-4) (1) =
 ? List matches (y/n) (y) = 
 ? The sequence is linear (y/n) (y) = n
 ? Search for definite matches (y/n) (y) = 
 Working
  Matches found=     2
      Name            Sequence                       Position Fragment lengths
    1 p               gaccatg'                           6225   7225     24
    2 p               ccc'ggg                            6249     24   7225

Finding the vepe values for the reverse primer in a single step. This gives us the position of the cloning site (6249) and the relative position of the primer site (-24).

Screening for Restriction Sites

If restriction enzymes sites have been used to cut the target DNA into random fragments it can be helpful to screen for their presence in sequence readings. The restriction site recognition sequences (not the enzyme names) are stored in a simple text file, left justified, one sequence per record. Readings are processed in batches whose names are stored in a file of file names "Input file of file names". The names of the readings that do not contain any of the recognition sequences are written to an output file of file names "Output file of passed file names", and those that do are written to "Output file of failed file names". The recognition sequences are read from "Input file of recognition sequences". Typical dialogue follows.

 vepe v4.0: vector excising program. May 95
 Select task
 X  1 Mark sequencing vector
    2 Mark cloning vector
    3 Check for vector rearrangements
    4 Check for restriction sites
 ? Selection (1-4) (1) =4
 ? Input file of file names=files
 ? Output file of passed file names=passed.enzymes
 ? Output file of failed file names=failed.enzymes
 ? Input file of recognition sequences=enzymes
 >>>> Read number  1 length  536 
 xb54a3.s1
 ...