[BiO BB] DNA Strider

[Pooja Jain]

Hi Yannick,

Have you ever had a look at SimVector. Its a standalone tool and works
very well on windows and Mac OS X.

http://www.premierbiosoft.com/plasmid_maps/index.html

Its one of the most powerful vector map drawing tool, with great graphic
support. It is quite fast in opening any sequence from GenBank and to
present the sequence features in graphic format. Moreover you can export
the plasmid/sequence map to EPS, SVG and gif, jpeg and various other
formats. You can also use the customizable graphic designing options that
it provides. Apart from all these it has various other features but are
limited to cloning, vector designing and generating restriction maps, you
might want to explore.

For me it was most useful in constructing the restriction maps of my
cloning vector and resultant recombinant, before I actually performed the
experiment in my lab and to put the plasmid maps in my presentation.

Its not that expensive also !

I hope this helps.

-Pooja


> Hi,
> I'm a student in Bioinformatics and Modeling at a French engineering
> school in Lyon, France (http://biosciences.insa-lyon.fr). Currently in
> my last year, I'm currently doing a six month internship in a C.
> elegans lab at McGill University in Montreal.
> The lab's computer are Macs, and besides standard browsing, word
> processing and image processing, lab members also use them to aid them
> in their molecular biology work.
> One of the programs they use is called DNA Strider. This piece of
> software has not been updated in a long time (probably since Apple's
> System 6.x - window sizes are fixed to the small old mac screen size!)
> and could require a face-lift.
>
> In the lab, it is mainly used for managing and manipulating sequences
> of genes, primers and constructs. The main features of interest here
> are:
> 	- Sequence management
>      - Graphical (circular or linear) restriction maps of a given
> sequence (or part of it), showing restriction site data concerning the
> part or whole sequence (for each enzyme, you get the number of
> restriction sites, and the obtained fragement sizes)
> 	- Reverse complementary sequence
> 	- Quick and simple alignment between two sequences
>
> I've searched the web and could not find an all-in-one package that
> seemed as user friendly and coherent as DNA Strider. Individual web
> sites and software tools do offer these features, but
> 	- the internet is slow (you click and need to wait before getting your
> result)
> 	- having everything in one place is nice
>
> Sequence Analysis (for Mac OS X) http://informagen.com/SA/ seems to be
> aiming to do what DNA Strider does, but is still very young (and
> closed-source, but thats a different debate).
>
> http://www.mekentosj.com/ has some very nice tools as well, but they're
> very problem-specific.
>
> Have I missed something? Is there a really cool java app or web
> software (that I could install locally for speed) that would replace
> DNA Strider? What does your molecular biology lab use in for it's day
> to day work?
> Oh and buying something expensive is not a solution.
>
> Thanks for any leads,
>
> Yannick.
>
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