[BiO BB] DNA Strider

Ryan Golhar ryangolhar at hotmail.com
Tue Mar 30 18:30:36 EST 2004

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

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 
	- 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 
	- 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,


\\  http://yannick.poulet.org icq: 22044361
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