New DNA manipulation program (freeware)

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loustau
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New DNA manipulation program (freeware)

Post by loustau » Wed Oct 10, 2007 1:27 pm

Hello all,

I have been doing a lot of cloning in the last ten years, and even though there are a few good free softwares available out there, there were many functions that I thought were missing from them.

Will the help of one of my friends who is in computer sciences, I decided to try my hand at programming and designed/wrote a program with what I considered were the most important and missing features ( within the limits of my capacities :) )

The result came out quite good, and I am using it a lot. With the help of the university I set up a website where it can be downloaded for free, for those who would be curious to give it a try. It works for Mac and PC.

It's called "PlasmaDNA", you can Google it since I can't post links yet.


Feedback or comments welcome!

Alexandre

P.S. There is also a short publication that describes the program, in BMC Molecular Biology.

Lukero
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Post by Lukero » Sun Oct 14, 2007 3:01 am

That sounds good. I'm going to try it out thanks

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Dustfinger
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Post by Dustfinger » Tue Oct 16, 2007 11:11 am

What can the program do ?
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MrMistery
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Post by MrMistery » Tue Oct 16, 2007 1:47 pm

Not bad. Might be useful someday
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victor
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Post by victor » Sat Oct 20, 2007 4:39 am

I've downloaded it and have tried it. I think it's a great program, even though I haven't get it all tried and haven't understand some of them :razz:
I think I'll also give this program to my professors :D

Thanks for the program, Dr. Alexandre Angers-Loustau :D
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loustau
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Post by loustau » Mon Oct 22, 2007 6:49 am

Dustfinger wrote:What can the program do ?


It analyses DNA sequences and draws the restriction map. This is pretty standard, but you can then use these enzymes to digest the DNA, and the digested fragments appear as separate sequences in the session, keeping in memory the overhangs generated. You can then ligate compatible fragments together and the resulting sequences are automatically generated.

You can also stimulate PCR, and looks for various common domains (like resistance genes, promoters, etc) for each sequence you enter and draws the map for you. You can expand all the databases to fit your need.

Basically, I use it to simulate the cloning I am about to do, from beginning to end, before starting on the bench. It also makes sure that I don't need to copy/paste anything to get the resulting sequences. That was the basic idea. I am adding features as I go depending on whether I figure out how to do them :)

victor wrote:I've downloaded it and have tried it. I think it's a great program, even though I haven't get it all tried and haven't understand some of them :razz:
I think I'll also give this program to my professors :D

Thanks for the program, Dr. Alexandre Angers-Loustau :D


You are most welcome :)

If you have question or need any help, don't hesitate to e-mail me!

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mith
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Post by mith » Mon Oct 22, 2007 4:11 pm

if you can make something that rivals sequencher, my boss would love you. They made him pay like 5000 dollars for a license.
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loustau
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Post by loustau » Tue Oct 23, 2007 11:41 am

Sadly, sequence alignment algorithms are way out of my league... :P

I heard from a laboratory that my program helped them save on GCK, another program with an expensive license. I am not familiar with it, and I can't imagine that it replaces it completely... I guess it depends what functions you use.

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mith
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Post by mith » Tue Oct 23, 2007 8:54 pm

Really? You don't have to make it totally accurate, just have it do pairwise instead of multiple. My prof showed us a perl script for it and it didn't seem too complicated.
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victor
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Post by victor » Thu Oct 25, 2007 9:17 am

oh, by the way....do anyone have a program for organic chemistry? :razz:
especially that capable for showing structure from the name that we type along with several 3D structures and projections.
Actually I have one, which is ChemDraw3D by CambridgeSoft but is there any other else? :razz:
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Post by blcr11 » Fri Oct 26, 2007 5:03 am

The free version of ChemSketch from ACD Labs is pretty good.

http://www.acdlabs.com/

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Post by Antonio_Leung » Sun Oct 28, 2007 3:21 am

I hava downloaded it. I think it can help me do something. thank you!

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