[BiO BB] DNA Strider

[Joel Dudley]

Several such systems are already under development and released in the private sector. I know of a soon to be open-source project that has all of these features and is already quite mature. You should hear about it in a month or so.
 
- Joel

	-----Original Message----- 
	From: bio_bulletin_board-admin at bioinformatics.org on behalf of Marcos Oliveira de Carvalho 
	Sent: Tue 3/30/2004 5:21 PM 
	To: bio_bulletin_board at bioinformatics.org 
	Cc: 
	Subject: Re: [BiO BB] DNA Strider
	
	


	It would be nice to have a bioinformatics IDRE ( Integrated Development
	and Research Environment) with some basic features (sequence
	visualization, editing, annotation, data management, etc...) and a well
	designed plug-in API, for easy extension. An idea could be build it on top
	of the NetBeans platform , and with java we get platform-independent
	software. (with other languages too, but java do the job)
	One can suggest add bindings with python/perl/ruby/java and theirs Bio*
	libraries, interfaces  to bioinformatics tools, including output capture
	(emboss, phred, phrap, BLAST, FASTA, Clustal,R/bioconductor, Mummer,...) .
	Also interfaces to webservices and data retrieving from major databases.
	Well, there are lots of possibilities.
	
	cheers
	Marcos
	
	
	
	On Tue, 30 Mar 2004 18:30:36 -0500, Ryan Golhar <ryangolhar at hotmail.com>
	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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	--
	"Science knows no country, because knowledge belongs to humanity, and is
	the torch which illuminates the world. "
	Louis Pasteur
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