WebDSV is an online DNA sequence editor and map drawing program. It provides basic analysis of DNA sequences (restriction sites, GC content).

A user can mark sequence features and visualize them along the sequence and in feature map.

WebDSV can be used to perform plasmid cloning in silico, design PCR primers, or to plan a gene synthesis.

Useful for molecular cloning and synthetic biology.

Online program to open GenBank files.

Online program to draw map from a GenBank file.

Successor of molecular cloning help.

An online plasmid editor software.

An online DNA software.

Molecular biology freeware.

WebDSV@molbiotools.com

2.0
quick hints genetic code genetic code compatible ends useful linx send feedback user guide
Display quick hints Display standard genetic code IUPAC ambiguous/degenerate positions Enzymes producing compatible ends Useful links Send feedback! User guide

Resize the application

Open a new WebDSV window

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linear circular

length:

Save Fasta
Save GenBank
Edit
Hide

SEQUENCE INFORMATION (GenBank file header)

Locus (or name):
Definition:
Length:
Linear/circular:
Accession:
Version:
Source:
Comment:

A > a
a > A
Crop
Rev. Complement
Select All
Translate Rev.
Translate
Rev. Primer
Forw. Primer
Add Feature
Selection: - 0 bp %GC
AA NNN
EcoRI NNN
NNN
>
>
Apply & Process
Undo Changes
Reverse Complement
Clear All
View Example
Sequence:
Restriction Site:
Clear Search
Find Rev Compl
Find


RESTRICTION ENDONUCLEASES

To display the cutting pattern and positions, doubleclick the enzyme name. To apply changes made in the selection, press 'Enter' key or click the 'Apply' button.

QUICK HINTS

  • Basic sequence handling:
    • Paste a DNA sequence in the editor field, open a sequence file, or download a sequence from GenBank.
    • Edit the sequence in the editor field as required, click 'Aplly & Process' after each step.
    • To mark a feature, first select the feature sequence in the editor field then click 'Add Feature'. Edit the feature type and visualization settings in the feature panel.
    • To save a sequence with marked features, use the 'Save GenBank' button.
  • Tips for efficient work
    • The visualization field cannot be used for editing. However, you can easily select a nucleotide position of interest in the editor field by doubleclicking the corresponding nucleotide in the visualization field. Use Ctrl+doubleclick to select spans of nucleotides. Similarly, doubleclicking an amino acid symbol, restriction site or feature label will select the corresponding sequence in the editor field.
    • To perform in silico molecular cloning, doubleclick the first restriction enzyme name in the visualization field, press Ctrl key and doubleclick the second restriction enzyme name. The corresponding DNA fragment will get selected in the editor field. Now you can use Ctrl+C and Ctrl+V for copying the fragment's sequence and pasting it into a target vector sequence already open in another WebDSV browser tab or window.

SETTINGS

Basic settings

Restriction sites:

display all sites
display only unique sites
display sites with maximum occurences


Restriction sites blocked by methylation (Dam or Dcm):

display and take into account
ignore

Genetic code:

Copy other genetic codes from the Genetic Codes NCBI webpage.



Primer multi-match detection limit:

nucleotide perfect match at 3' end



Appearance

Font sizes in the visualization field:

normal
large



Map drawing settings

Feature labels in maps:

with position values
without position values


Restriction sites in maps:

with position values
without position values


Basic circle diameter in plasmid maps:

small
medium
large


Inside plasmid maps show:

plasmid name and length
1000 bp scale


In plasmid maps, group restriction sites to list blocks if:

At least restriction sites are detected
within a range of no more than nucleotides.



STANDARD GENETIC CODE

genetic code

IUPAC AMBIGUITY CODE

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

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

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DISCLAIMER: This free software comes without any warranty. The author of the software bears no responsibility for any loss or damage that may arise from its use for gene synthesis design or any other purpose.

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