How To Visualize Restriction Cutting Sites On Sequence?

Question

[BioInfo1010]

I have restriction cutting sites for many restriction enzymes. I want to represent this sites diagrammatically. Which tool/software should I use to show this cutting sites on the sequence.

[es_saberi]

Hi

I want to do Virtual RFLP analysis on 16Sr DNAsequences from different isolates

Using the virtual gel plotting program pDRAW32 (AcaClone). actually I want to generate pattern of enzymatic restriction of all sequence with each one of restriction enzymes (AluI, BamHI, BfaI, BstUI, DraI,EcoRI, HaeIII, HhaI, HinfI, HpaI).

it is gratefully appreciated if you write me the path.

Sincerely yours

esmaeil

email: [e-mail]

Answer 1

[Anima Mundi]

Hello, you could use pDRAW32 (freeware), Serial Cloner (freeware), ApE Plasmid Editor (freeware), VectorNTI, MacVector, depending on your preferences and on the OS you are working on. Personally, for what you ask I would simply use pDRAW32.

[BioInfo1010]

Thank you very much.

Actually I have name of restriction enzyme and cutting sites in a text file. I want to visualize by diagrammatically on web page.

e.g.

EnzymeName        Cuttingposition
HindIII                    27,
HindIII                    42,
HindIII                    56,
HindIII                    73,
HindIII                    87,
EcoRI                    17,
EcoRI                    27,
EcoRI                    33,
EcoRI                    37,
EcoRI                    49,
......................................

like this many enzymes and their restriction cutting site. I want to visualize this on the sequence. is there any tool/software/java,perl script for visualize on web page.

Thank u again for your help.

[Anima Mundi]

Ok, in that case I guess Matt provided the desired answer ;).

Answer 2

[Matt Shirley]

I would suggest NEBcutter. It is a web-based tool from New England Biolabs, and will generate a map cut sites for your sequence and enzymes.