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User guide
Silent Mutator - Silent mutagenesis tool
View Example
A gene synthesis tool, with which you can easily introduce new restriction sites without changing the amino acid / protein sequence.
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The genetic code used for translation of the input sequence is selected from the dropdown menu.
Should other genetic code be used, a user can modify one of the selectable genetic codes by first selecting
particular genetic code from the menu and then changing the selection to "User Provided".
The genetic code table can be completely replaced, but the format must stay exactly the same.
One can find and copy-paste genetic codes from the Genetic Codes NCBI webpage.
SETTINGS
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The sequence is:
Restriction sites:
Dam/Dcm-methylated sites:
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Genetic code:
(display)
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Save Fasta
Plain text, fasta or GenBank formats.
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Plain text is just text without any formatting (i.e. from e.g. Notepad, but not MS Word).
A fasta file is plain text sequence with a header in the form ">sequence name".
A GenBank file contains a nucleotide sequence plus related information and feature definitions.
FILE INFORMATION
| Sequence Name: | |
| Linear/circular: | |
| Length: | |
| Accession: | |
| Source: |
Translate &
Analyze
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Selection:
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0 bp
%GC
Clear All
Apply & Process
Undo Changes
View Example
All
fields will be erased, unsaved work will be lost!
Sequence:
Restriction Site:
Restriction Site:
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Restriction Endonucleases
To display the cutting pattern and positions, double-click the enzyme name.
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Restriction endonucleases
To display the cutting pattern and positions, double-click the enzyme name. To apply changes made in the selection, press 'Enter' key or click the 'Apply' button.
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Quick hints
- Basic worflow:
1. Paste a DNA sequence in the editor field or open a sequence file.
2. Modify settings as needed.
3. Select the coding part of the sequence.
4. Click the Translate & Analyze button.
5. Inspect results in the restriction sites table and in the graphical output. Move mouse pointer over the restriction site names for additional information. - Executing silent mutagenesis:
1. double-click the restriction enzyme name in the tabular results.
2. Click the position of interest among the cyan-marked ranges.
3. Click the Apply & Process button.
4. The sequence now contains the new restriction site and is ready for further silent mutagenesis or to be saved in a file. - If any manual editing is done in the editor field, click the Apply & Process button before performing translation and analysis.
Standard Genetic Code
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IUPAC Ambiguity Code
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| Symbol | Bases represented | Complement |
|---|---|---|
| R | A, G | Y |
| Y | C, T | R |
| K | G, T | M |
| M | A, C | K |
| S | C, G | S |
| W | A, T | W |
| B | C, G, T | V |
| D | A, G, T | H |
| H | A, C, T | D |
| V | A, C, G | B |
| N | A, C, G, T | N |
Compatible Ends
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| Overhang | Enzymes |
|---|---|
| N│G A T C N N C T A G│N | BamHI, BglII |
| N│A A T T N N T T A A│N | EcoRI, MfeI (MunI) |
| N│T C G A N N A G C T│N | SalI, XhoI |
| N│C T A G N N G A T C│N | AvrII (XmaJI), NheI, SpeI (BcuI), XbaI |
| N T G C A│N N│A C G T N | NsiI (Mph1103I), PstI |
| N│G T A C N N C A T G│N | Acc65I (Asp718I), BsiWI (Pfl23II), BsrGI (Bsp1407I) |
| N│C C G G N N G G C C│N | AgeI (BshTI), BspEI (Kpn2I), XmaI (Cfr9I) |
| N│G G C C N N C C G G│N | EagI (Eco52I), PspOMI (Bsp120I), NotI |
| N│C G C G N N G C G C│N | AscI (SgsI), BssHII (PauI), MluI |
| N N│C G N N N N G C│N N | AclI (Psp1406I), BstBI (Bsp119I), ClaI (Bsu15I), NarI |
| N N│T A N N N N A T│N N | AseI (VspI), NdeI |
| N N A T│N N N N│T A N N | PacI, PvuI |
| blunt ends | AfeI (Eco47III), BsaBI (BseJI), DraI, EcoRV (Eco32I), Ecl136II, FspI (NsbI), HpaI (KspAI), MscI (MlsI), NaeI (PdiI), NruI (Bsp68I), PmeI (MssI), PmlI (Eco72I), PvuII, ScaI, SfoI (EheI), SmaI, SnaBI (Eco105I), SrfI, SspI, StuI (Eco147I), SwaI (SmiI), XmnI (PdmI), ZraI |