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  • Recut - Predicting restriction enzmyme digests

    Sample In | Sample Out | Download (25.1 KB Zip File)
    Instructions

    First set up your input sequence file using notepad. Copy and paste the sequences from Editseq or other file format. The input file must have the following format:

    Line 1 		title
    Line 2 		allele name (OTU name)
    Line 3 and on	Sequence in upper case letters
    A,T,C,G,N (missing data), and '-' for deletions
    sequence must end with ;
    Later Line 		next allele name
    Later line +1 	next sequence, end in ;
    And so forth
    

    Example sequence data is the file pcr1.txt

    Make sure there should be no blank lines after the last semicolon.

    To execute

    Start the command prompt and go to the directory with your input sequence file.
    Type 'recut' and respond to queries.

    To add new enzymes

    Recut reads the text file called 'recut.tab' to obtain the list of enzyme to test. To add a new enzyme of change this list, edit the recut.tab file in notepad. Change the number of enzymes in the first row to the appropriate number to be read. Add the enzyme name, length or the recognition sequences, and the sequence itself to the list. Keep the exact column format. Extra enzymes can be kept in the table beyond the end of the list.

    Example output

    Open the output file with notepad. Recut lists the restricion enzyme infoamtion first, then the number of cuts for each sequence. The fragment sizes are given from the beginning to the end of the sequences as cut sites are found, i.e. the first fragment goes from the start of the sequence to the first site.

    Contact stec@cvm.msu.edu
    Operated by Shannon D. Manning at Michigan State University