[BiO BB] DNA Strider

[Gary Van Domselaar]

Hey Gang,

For platform-independant sequence _manipulation_ there is the sequence 
manipulation suite:

http://bioinformatics.org/sms2

SMS2 and EMBOSS together cover most of what you can expect to get out of 
an old sequence analysis package like DNA strider.

Decidedly,

g.



On Tue, 30 Mar 2004, Iddo Friedberg wrote:

> 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
> > 
> > _______________________________________________
> > BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > _______________________________________________
> > BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > 
> > 
> 
>