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Jalview - a java multiple alignment editor
(Experimental pre-beta release)
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*** 14/5/98 New speedier display (3x on my R10k) ***
JalView is being used in:
Use JalView to view your own alignment here. (New 4th June 1998)
Introduction and features
Jalview is a multiple alignment editor written entirely in java.
It was initially to be used as a visualization tool for the Pfam
CORBA server and client at the EBI
but is available as a general purpose alignment editor.
Jalview's features include:
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Variable font sizes/colours
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Colour by amino acid physio-chemical property,
similarity to consensus sequence, hydrophobicity or secondary structure.
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Sequences can be grouped and coloured differently.
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Smith Waterman pairwise alignment of selected
sequences
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Sort sequences by pairwise identity to
consensus or selected sequence.
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Consensus sequence calculations
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Removal of redundant sequences (coming
soon).
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Gaps can be inserted/deleted using the
mouse.
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Input from URL/local file (if running as
application ) or cut and paste in textbox
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Common formats supported - msf,fasta, clustal.
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Text output via email/browser.
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Links to swissprot SRS server at EBI.
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Colour postscript output via email
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HTML parameters let you input sequences
and groups and colour schemes.
Why write a multiple alignment editor? There are certainly good programs
out there (e.g. seaview and Cinema and a very special mention for belvu
even though it's not an editor) but none of them have all the features
I want. I wanted to combine display speed and consensus colour
schemes with easy access to the databases available on the internet
using CORBA or CGI.
The ability to run java applets in web browsers is probably the most
important reason for using java as it enables the software to be easily
accessed from almost anywhere and easy integration with sequence databases
available on the web. The speed of the java VMs is improving and
much helped by just-in-time compilers although java can not claim to be
winning any points for speed of execution.
Gripes (minor of course)
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Even though things have improved the display speed is not as fast as desired
when running the editor through a web browser. This is much
more acceptable when it is run as an application. I'm still working
on the speed - sequence groups are slowing things down at the moment but
an upgrade is coming.
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There is not as much flexibility in the colour schemes and a choice of
scoring matrices is not included.
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Only basic editing is supplied - can't delete residues, no group editing
Further information available from M.Clamp
Last update 15th April 1998