[BiO BB] DNA Strider

[Iddo Friedberg]

Hi Ryan,

EMBOSS works on Un*x, Linux and FreeBSD machines, and on Mac OS-X, so 
that covers everything but Windows.

http://emboss.org

Apparently you can get full functionality using Cygwin in Windows, or

there is an EMBOSS for Windows project going on,

http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html

Seems to be alive, their latest update is from 02/04. They claim to have 
158 programs from the original EMBOSS suite implemented.

JEMBOSS is the Java-based point-and-click interface, works on Linux, Mac 
OS-X, AND Windows.

Cheers,

Iddo


Ryan Golhar wrote:
> You know, I'm constantly finding different programs to perform different
> tasks.  Either client applications, or web-based.  Some run on Linux,
> others Windows.  
> 
> I would like to see 1 application for multiple platforms to performs dna
> sequence analysis.  I started writing something in Java to do this but
> haven't touched in awhile.
> 
> I'm wondering how many people would be interested in helping to develop
> a  platform-independent application to perform all sorts of sequence
> analysis - alignments, snp analysis, assembly, etc.  Sort of like GCG,
> but free and actually user-friendly and useful.  If people are
> interested, I think we should talk about a framework and start building
> something as needed.  
> 
> Any comments?
> 
> -----
> Ryan Golhar
> Computational Biologist
> The Informatics Institute at
> The University of Medicine & Dentistry of NJ
> 
> Phone: 973-972-5034
> Fax: 973-972-7412
> Email: golharam at umdnj.edu
> 
> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of
> Yannick Wurm
> Sent: Tuesday, March 30, 2004 10:05 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] DNA Strider
> 
> 
> 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.
> 
> \\\\\\\\\\\\\\\\\\\
> \\  http://yannick.poulet.org icq: 22044361
> \\  idh at poulet.org  tel: ++33.6.16.41.71.92
> 
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-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo