[BiO BB] DNA Strider

Marcos Oliveira de Carvalho operon at www.ufsm.br
Tue Mar 30 19:21:28 EST 2004

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.


On Tue, 30 Mar 2004 18:30:36 -0500, Ryan Golhar <ryangolhar at hotmail.com> 

> 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: ++
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