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Easier DNA Sequence Manipulation

Content sponsored by New England Biolabs

Easier DNA Sequence ManipulationIf you regularly use online DNA sequence manipulation programs, your life might be about to get just a little easier.

At Bitesize Bio, we were becoming tired of jumping from site to site to get the sequence manipulation tools we needed. One site for reverse complementation, another for translation and yet another for restriction analysis… it was all just a bit irritating.

So we decided to team up with Alexandre Angers-Loustau, creator of the superb cross-platform plasmid analysis package, PlasMa DNA, (I mentioned this in a previous article). Alexandre is in the process of creating a javascript application that combines all of your sequence manipulation needs into one handy multi-tool.

With version 1.0 you can clean up, reverse complement, translate and restriction analyze your DNA sequence, all from one window.

We think this tool is fast, user-friendly, and provides a great alternative to trawling through your bookmarks to load up individual tools on different sites. Take a look, and tell us what you think.

Alexandre is already hard at work on the next version,  which will have even more great features. And and we’d like you to join in the fun by telling us about features you’d like to see in future versions, or any ways in which you think the current version can be improved.

Just drop us a quick line via our contact page to tell us your thoughts. As ever, we look forward to hearing from you.

We’ll keep you informed whenever new versions of this excellent tool are released. Happy sequence manipulation!

9 Comments

  1. Vladimir on April 5, 2016 at 10:19 pm

    I suggest WebDSV as an alternative. It is a free web app providing all the essential functionalities – DNA sequence editing, feature management, and map drawing. It works the same on all platforms (Windows, Mac, Linux) and uses the universal GenBank format.
    http://www.molbiotools.com/WebDSV/index.html

  2. Evelyn on December 31, 2009 at 4:20 pm

    Nick,

    I read your posts about PlasMa DNA software and I would like to tell you about BxSeqTools. Clean up, reverse complement, translate and restriction analyse your DNA sequence, all from one window BUT they offer importing files directly from GenBank, provide a personal database on which you can store your data, and since the software is web-based, there is no software to install! Its free for individual users. Try the demo at http://www.bioinfoman.com or look at the web demos on YouTube http://www.youtube.com/user/BioInfoManagement.

  3. Jode on November 26, 2009 at 4:11 am

    Has the multi-tool page been taken down?

  4. Nick on March 11, 2008 at 5:06 pm

    Hi Max,

    If you don’t already have javascript installed you’ll need it for the tool to work. You can download it at http://java.com/en/download/index.jsp

  5. Max on March 10, 2008 at 4:57 pm

    Can not see or use the multitool. The page is empty. I am using firefox 2.0.0.8 on linux.

    Are there any specific requirements?

  6. Alexandre on March 10, 2008 at 10:12 am

    Patrick, I am aware of Vector NTI, and other very good free programs (ex. pDRAW). Since I don’t think a single week went in the last 12 years without me doing some cloning, I decided to try my hand at my own program which would really target what I need.

    I’m not selling anything, and it’s hard to say if PlasmaDNA is better than this or that. I can’t compete with the programming skills of professional programmers, but a program designed from scratch by a direct user does have some important advantages – feel free to give it a try, maybe you’ll like it too.

    To Kurt, version 1 is barebone, and will improve quickly. Again, we are not filling a gigantic void, just adding options so that people can choose which tool kit they prefer.

  7. Nick on March 10, 2008 at 9:31 am

    @Patrick. Thanks for this. Vector NTI is indeed a great program. However, I personally like web-based applications for performing simple manipulations because they can be run from any computer quickly and easily.

    Our aim is to create a feature-packed but light and user friendly utility for users who, for whatever reason, like to use web-based applications for sequence manipulation.

    Also, as far as I am aware, Vector NTI is free for academics only, not for commercial companies.

    @Kurt At the moment the only benefit I think we have compared to sites like SMS is that our multi-tool is a bit easier to use since all functions are run from one java applet.

    You just have to paste your sequence in once, then you can do all of the available manipulations on it. With SMS you have to switch between applets and re-enter your sequence to perform different function.

    Also bear in mind that this is just version 1.0. We have many more functions and features planned, which we will be implementing in future versions that will make this an excellent tool.

    As I said in the article, we hope that our readers will help us to shape future versions of the tool by telling us what features they’d like to see implemented.

  8. Kurt on March 10, 2008 at 6:03 am

    What is this contributing compared to e.g. SMS?

    http://www.bioinformatics.org/sms2/

  9. patrick on March 10, 2008 at 1:59 am

    VectorNTI v10.3 (download and license free from Invitrogen) is an superb suite of programs for sequence manipulation, including alignment, restriction analysis, blast searches, plasmid construction, gateway cloning, etc. It uses one coherent database for both nucleotide and amino acid sequences.

    FWIW.

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