A tool for generating DNA MTase motif testing sequences
DNA methyltransferase binding motif plasmid assembler
- To identify the motifs of multiple DNA methyltransferases (DNA MTase) simultaneously.
- This script requires python 3.6 or newer.
- Install using "pip install metmap"
- This will put a script named "run_metmap.py" in your pythons bin folder.
- Linux: You should just be able to type "run_metmap.py" from terminal
- Windows: The script will be placed in your python folders "Scripts" subfolder and you can run it with "python path\to\python\Scripts\run_metmap.py" from command line
- Mac: Who knows..probably works like linux?
You can download the tests/test_data.txt and run
This should generate a cas1.fa and cas1.gb file.
- You have an organism with multiple identified DNA MTases and you wish to know their individual motifs.
- You use NGS to obtain motifs of all methylated DNA sites.
- Some of those motifs will contain ambiguous bases and some will not
- You submit those motifs to this program
- This program then stitches these motifs together in random order
- Motifs may contain ambiguous bases per the IUPAC nucleotide code
- We can't synthesize lots of ambiguous bases, so we "de-ambigulate" them before putting them into the final construct.
- De-ambigulation happens according to 1 of 2 rules:
- Rule 1:
- Pick L random variants of the motif. E.g. Motif ATGNNTTA have a total of 16 possible actual sequences. If L<16 then the program will random pick L variants (without duplicates). If L>16 then each possible variant will be picked at least L/16 times and some will be picked 1 more than that.
- Rule 2:
- Make K copies of each completely "de-ambigulated" variant: E.g. the sequence "SATC" will then be treated as 2 sequences: "GATC" and "CTAC" that will each appear in K copies.
- Rule 1:
- We put M N's between each motif
- And the program will output P versions of these cassettes
- You then clone this cassette into a plasmid with 1 DNA MTase in each plasmid.
- You then transform this library into an organism that doesnt natively methylate DNA.
- Grow, Harvest, Sequence plasmids.
Motif file format
- The motifs should be stored in a standard text file
- One motif per line, then a comma then a 1 or a 2 to indicate whether either rule 1 or 2 should be used for this motif
IUPAC nucleotide code:
|R||A or G|
|Y||C or T|
|S||G or C|
|W||A or T|
|K||G or T|
|M||A or C|
|B||C or G or T|
|D||A or G or T|
|H||A or C or T|
|V||A or C or G|
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