MitoEdit Logo
About MitoEdit

Follow these steps to analyze your DNA sequence:

  1. Enter Position: Specify the 1-based position of the base you want to target in your DNA sequence.
  2. Select Reference Base: Choose the original base (A, T, C, or G) at the specified position.
  3. Select Mutant Base: Choose the desired base conversion (A, T, C, or G).
  4. Upload DNA Sequence (Optional): You can upload your own DNA sequence file (.txt or .fasta format). If not provided, the human mitochondrial DNA sequence will be used by default.
  5. Analyze Sequence: Click the "Analyze Sequence" button to start the analysis.
  6. View Results: Once the analysis is complete, you can download the results as an Excel file containing:
    • Target windows for each applicable editing pipeline
    • Optimal TALE sequences for targeting
    • Potential bystander edits and their effects
    • Target and bystander bases marked with brackets ([ ] for targets, { } for bystanders)
Examples
Example 1: Targeting human mitochondrial DNA

Input:

  • Position: 11696
  • Reference Base: G
  • Mutant Base: A
  • DNA Sequence: Default human mtDNA

Expected Output:

An Excel file named final_11696.xlsx with two spreadsheets:

1. All_Windows Sheet (first few rows):

Pipeline Position Reference Base Mutant Base Window Size Window Sequence Target Location Number of bystanders Position of Bystanders Optimal Flanking TALEs Flag (CheckBystanderEffect)
Mok2022_G1397_DddA11 11696 G A 14bp GCA[G]TCATT{C}TCAT Position 4 from the 5' end 1 [11702] FALSE -
Mok2022_G1397_DddA11 11696 G A 14bp CGCA[G]TCATT{C}TCA Position 5 from the 5' end 1 [11702] FALSE -
Mok2022_G1397_DddA11 11696 G A 14bp GCGCA[G]T{C}ATTCTC Position 6 from the 5' end 1 [11698] FALSE -
Mok2022_G1397_DddA11 11696 G A 14bp GGCGCA[G]T{C}ATTCT Position 7 from the 5' end 1 [11698] FALSE -

2. Bystanders_Effects Sheet (first few rows):

Bystander Position Reference Base Mutant Base Location On Genome Predicted Mutation Impact SNV Type AA Variant Functional Impact MutationAssessor Score
11698 C T Complex 1 Predicted Benign synonymous SNV V313V
11702 C T Complex 1 Predicted Pathogenic nonsynonymous SNV V315F medium 3.44
11704 C T Complex 1 Predicted Benign synonymous SNV V315L
Example 2: Targeting custom DNA sequence

Input:

  • Position: 33
  • Reference Base: G
  • Mutant Base: A
  • DNA Sequence: Custom file (test.txt)

Expected Output:

An Excel file with one spreadsheet:

All_Windows Sheet (first few rows):

Pipeline Position Reference_Base Mutant Base Window Size Window Sequence Target Location Number of bystanders Position of Bystanders Optimal Flanking TALEs Flag_CheckBystanderEffect LeftTALE1 RightTALE1 LeftTALE2 RightTALE2
Mok2020_G1397 33 G A 14bp ACTG{G}[G]AGAACTCT Position 6 from the 5' end 1 [32] FALSE TRUE
Mok2020_G1397 33 G A 14bp TG{G}[G]A{G}AACT{C}TCT Position 4 from the 5' end 3 [32, 35, 40] FALSE TRUE
Mok2020_G1397 33 G A 14bp CTG{G}[G]A{G}AACTCTC Position 5 from the 5' end 2 [32, 35] FALSE TRUE
Mok2020_G1397 33 G A 14bp TACTG{G}[G]AGAACTC Position 7 from the 5' end 1 [32] TRUE TRUE T TACCCCCCACTATTAACC TCTGTGCTAGTAACC A T ACCCCCCACTATTAACC TCTGTGCTAGTAACC A

Note: When optimal flanking TALE sequences are found, they are added to the LeftTALE and RightTALE columns. The impact of bystander edits is not provided when using a custom DNA file.

Note: The analysis may take a few minutes to complete, especially for longer sequences.
Enter the position of the base to target (1-based index)
Select the original base at the specified position
Select the desired base conversion
Upload a DNA sequence file (.txt or .fasta). If not provided, human mtDNA sequence will be used.

Processing sequence... This may take a few minutes.

Results
{% include 'footer.html' %}