[Biojava-l] Multiple Sequence Alignment Viewer

[Phillip Lord]

>>>>> "Nathan" == Nathan Whitehouse <nlwhitehouse at yahoo.com> writes:

  Nathan> Dear all,
  Nathan>   I've used biojava on and off for some time, and I've
  Nathan>   always found it
  Nathan> useful.

  Nathan>   I'm not sure how to proceed with my current problem,
  Nathan>   though I'm sure
  Nathan> someone has done it already.
  
  Nathan>   I basically need a way to visualize a set of sequences
  Nathan>   which need to
  Nathan> be aligned.

  Nathan>   Can anybody point me in the right direction on this?  Is
  Nathan>   there an easy tool to visualize multiple alignments?


There are a number of multiple alignment viewers available, in java,
although none are based on biojava that I know of. 

You could look at Cinema of which there are two versions

http://bioinf.man.ac.uk/dbbrowser/CINEMA2.1/
http://www.russet.org.uk/cinema.html

The second one I wrote. At some stage it would be nice to port it to
biojava, which should be possible, as its underlying representation of
sequences is relatively similar to biojava. The first is more mature
though, and has more features.  

Also is strap, which again has some nice features, although I have
found it fairly hard to use. 

http://www.charite.de/bioinf/strap/

And finally on the Java front would be jalview, which is probably the
most widely used, and which someone else has already posted a url to. 

On the non java front yet another version of Cinema, also from
Manchester, is worth a look, which comes as part of the utopia
project. Its written in C, and used Qt, as a toolkit if memory serves
me well.

http://aig.cs.man.ac.uk/utopia/

This has the advantage that its been designed by visualisation
experts. I would be prepared to admit that the user interface design
improves on my own version of Cinema significantly. I'm far to polite
to compare it to other peoples editors. I'm not sure whether there is
a download URL for this at the moment, but I've cc'd the authors on
this email. 

There is even one for emacs, if this is your thing.

http://www.red-bean.com/ale/

And a couple more of varied ages, which you can get references for,
from my paper. 

http://www.cs.man.ac.uk/~phillord/download/publications/cinema-paper.pdf

What a dizzying array of options!

Cheers

Phil


-- 
Phillip Lord,				Phone: +44 (0) 161 275 6138
PostDoctoral Research Associate,        Email: p.lord at russet.org.uk
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