[BiO BB] DNA Analysis Open Platform (was: DNA Strider)

JRambla jrambla at hotmail.com
Tue Apr 6 12:16:01 EDT 2004


Sorry for asking,

What's the difference of this proposal with the JEMBOSS project? More depth
in some areas? More features?

Jordi Rambla
Barcelona (Spain)
 

-----Mensaje original-----
De: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org] En nombre de LJ
Enviado el: miércoles, 31 de marzo de 2004 23:23
Para: bio_bulletin_board at bioinformatics.org
Asunto: RE: [BiO BB] DNA Strider

i like this idea quite a bit. i know several programmers/bioinformaticists
who might want to help out. they are really impressed with python these days

lon james
postgres, inc
1 fair oaks
san francisco, ca 94110
415-573-9192
lon at efcodd.org

-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Ryan
Golhar
Sent: Tuesday, March 30, 2004 3:31 PM
To: bio_bulletin_board at bioinformatics.org
Subject: RE: [BiO BB] DNA Strider


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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