DNA sequence editing software

DNA online tools

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 as a feature map.

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

WebDSV is useful for molecular cloning and synthetic biology.

WebDSV is an in silico gene editing tool.

WebDSV is an online plasmid map drawing tool.

WebDSV helps to visualize GenBank files. It is an online program to draw a map of features from a GenBank file

online DNA software, online molecular biology applications

WebDSV is a general-purpose molecular biology freeware, a DNA sequence manipulation suite, free plasmid cloning software, vector design application, DNA cloning program.

WebDSV is an online plasmid editor software, app to draw a plasmid map. It is a successor of Molecular Cloning Help.

Gene synthesis design tool

WebDSV is a gene design software.

online app to design molecular cloning experiments, molecular cloning program, molecular cloning design

Molecular genetics software

WebDSV is a DNA sequence viewer and editor. It is an online program that can open and edit GenBank files.

WebDSV is a plasmid design program.

DNA sequence translation online tool

WebDSV is an online tool to translate a DNA sequence to protein. It can also translate the DNA sequence in reverse orientation.

DNA translation, DNA translator, free DNA tools

online DNA to protein translation tool

online protein translation tool, nucleotide-protein translation

DNA sequence reverse complement tool

transcription and translation sequence tool, translate tool

WebDSV can be used as an alternative to other software

  • alternative to APE plasmid editor
  • alternative to Clone Manager
  • alternative to Serial Cloner
  • alternative to Benchling
  • alternative to Genome compiler
  • alternative to Snapgene
  • alternative to Geneious
  • alternative to pDRAW32
  • alternative to DNA Lasergene
  • alternative to VectorNTI
  • alternative to Gene Construction Kit

It is a solution to plasmid mapping practice problems, an online vector editor. It facilitates DNA cloning design.

polylinker or multiple cloning sites region highlighting

restriction mapping of plasmid DNA

design PCR primers with restriction sites

design DNA cloning online

WebDSV is molecular biology software that allows users to plan, visualize, and document molecular biology procedures.

WebDSV contains a standard genetic code table.

WebDSV contains a table of compatible cohesive ends.

WebDSV@molbiotools.com

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

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linear circular

length:

Save as Fasta
Save as GenBank
Edit
Hide

SEQUENCE INFORMATION (GenBank file header)

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

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


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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.
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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.




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.



PCR primers

Primer multi-match detection limit:

nucleotide perfect match at 3' end


Tm calculation

Primer concentration (nM):
Total monovalent cation concentration (mM):
Mg2+concentration (mM):
Total dNTPs concentration (mM):




STANDARD GENETIC CODE

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GGU GGC GGA GGG AGU AGC AGA AGG Gly CGU CGC CGA CGG UGU UGC UGA UGG Ser Arg Arg Cys STOP Trp GUU GUC GUA GUG AUU AUC AUA AUG Val CUU CUC CUA CUG UUU UUC UUA UUG Leu Phe Leu Met Met Ile GAU GAC GAA GAG AAU AAC AAA AAG Asp CAU CAC CAA CAG UAU UAC UAA UAG Glu Asn Lys His Gln Tyr STOP STOP GCU GCC GCA GCG ACU ACC ACA ACG Ala CCU CCC CCA CCG UCU UCC UCA UCG Thr Pro Ser U C A G U C A G

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
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Real-time On-selection Calculations

WebDSV calculates the selected sequence length, GC-content, and predicted melting temperature in real time when the user is selecting a sequence in the Editor Field. The melting temperature prediction is limited to length interval 10 - 120 bp and is based on the nearest neighbor method with parameters described in SantaLucia 1998 (see the WebDSV manual for more details and a full reference).

Click the GC-content value to see a GC-content plot.

info@molbiotools.com


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.

New Feature
Autodetect
PCR Product
Map
Update
Start - end distance: nothing selected
Undo

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.

The restriction enzyme selection can be changed either manually with checkboxes located in the last column of the table or by loading the restriction enzyme list from a file with the Load List button. The file should be a plain text file containing one restriction enzyme name per line. You can write such file in MS Notepad or similar program or by saving the current selection with the Save List button. The Reset button will restore the default selection list. The Set Permanent button will store the present selection in the browser memory. The success of this operation depends on the particular web browser and its settings. If successful, the selection will be preserved in all new browser tabs or windows in the course of the present session. It, however, might not be available in future sessions, so saving the selection as a file is highly recommended.

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WARNING

The example sequence will replace the existing sequence. Continue anyway?

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