[BiO BB] What do you use for MSA and Design?

Harry Mangalam harry.mangalam at uci.edu
Mon Jul 10 12:53:32 EDT 2006

Hi Rick,

You don't say what kind of data you're importing, which will drive the 

If the info is available or if you can configure the eventual output, 
the clustal output format (.msa) is quite well-supported among 
downstream applications. If you're trying to maintain phylogenetic 
info, the Phylip format (.dnd) is well supported as well.  If you 
only have html output then you're in for some parsing.

I'm not familiar with GoCore output, but if it's a Excel-based format, 
you can extract the contents via perl's parseexcel modules altho 
complex links and structure will probably be lost.  On the other 
hand, most large-scale analyses don't relay on point&click apps as a 
part of the analysis for obvious reasons, so unless gocore provides 
some kind of exceptional analysis (it doesn't appear to, via an 
admittedly fast drive-by of the site), it's probably more appropriate 
to use one of the more programmable/scriptable analysis tools 
available to produce the data in the 1st place.


On Saturday 08 July 2006 08:39, Richard Colman wrote:
> I am currently working on a computer user interface for specifying
> (not designing) mutational protein libraries. In addition to a
> "online forms interface" I would like to be able to directly import
> protein sequence data and multiple sequence alignments from a file.
> I was wondering whether any researchers would like to comment on
> what types of programs and data formats are popular. In paticular,
> I am considering an function to directly import Excel spreadsheet
> files (ala GoCore, etc.), FASTA with alignments preserved, or ????
> Any comments would be greatly appreciated.
> Rick Colman
> UC Irvine
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Harry Mangalam - Research Computing at NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c) 
harry.mangalam at uci.edu

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