Inverting characters in multiple alignment

David S. Peterson dspete at helix.nih.gov
Wed Dec 21 08:55:07 EST 1994


In article <garrisonp.1138359321A at thorin.uthscsa.edu> garrisonp at UTHSCSA.EDU ("Preston Garrison") writes:


>I'm annotating a multiple alignment for publication, and I would like 
>to invert some characters (picked by me, not by an algorithm in an alignment
>program) to white on black, as is commonly done. Does anybody know of a Mac 
>program that can do this and print it to a Laserwriter? I have tried it in 
>Canvas 3.05, but it will only do it for an entire text object, not for 
>individual characters. (I assume this can be done in GCG, but I have been 
>avoiding having to learn to speak VAX.)

>Thanks,

>Preston Garrison                 garrisonp at uthscsa.edu
>Biochem. Dept.                   voice: 210-567-3702
>Univ Texas Health Sci Ctr        fax:   210-567-6595
>San Antonio, Tx 78284-7760
>USA

There is a program called DNADraw available in UNIX, Mac and DOS flavors that 
will allow you to shade or inverse any particular character in an 
alignment. It outputs a Postscript file, but all the shading must be done by 
hand, I don't believe you can input a partially shaded alignment. It should be 
available from either ncbi.nlm.nih.gov or dcrt.nih.gov. Also, there is a 
program called Boxshade which will automatically shade an alignment based upon 
a modifiable list of similar vs. conserved amino acids. It's available on many 
of the molecular biology ftp servers, but I believe only in a DOS or UNIX 
version. I've used it extensively in a semi-automatic alignment shading 
system. Basically I feed a multiple sequence alignment into Boxshade and have 
it output in RTF (Microsoft's Rich Text Format). I edit the RTF file in Word 
to add any additional shading or inverse text, then use a Word macro to turn 
the result into the "sequence" and "template" files expected by the UNIX 
version of DNADraw. Somewhat complicated, but once set up I can quickly redo 
the figure to change number of characters per line, something not easily done 
in a drawing program.

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