[ANN] Macboxshade v2.11 posted

michael.baron at bbsrc.ac.uk michael.baron at bbsrc.ac.uk
Tue Nov 3 10:24:53 EST 1998


MACBOXSHADE version 2.11 is now available from the BOXSHADE web page:

ftp://ftp.isrec.isb-sib.ch/pub/sib-isrec/boxshade/MacBoxshade/MacBoxshade_2.1.hqx


(N.B. same archive name as version 2.1, but new version!!!!)

MACBOXSHADE is a program for creating good-looking printouts from
multiple  aligned protein
or DNA sequences. The program does no alignment by itself, it has to
take as input a file
preprocessed by a multiple alignment program or a multiple file editor.

NEW in v2.11:
 fixes a long-standing, but only just discovered, bug whereby opening 
two ASCII display or two matrix display windows caused a crash 
(thanks to Dr. Todd Richmond, Carnegie Institution of Washington, for 
pointing the bug out to me).

NEW in version 2.1:

Wrote my own text display routines, so the 'current alignment' and
'Display ASCII' windows are no longer limited to 32 000 characters.

Modified the PICT display so that it would not be stuck in low memory
situations. If there is enough memory assigned to the program, you get
the nice, smooth-scrolling display as previously; if not, the program
tries to borrow more memory from unassigned RAM in your machine (if
any). If this, in turn, fails, you get a rather jerky, slow-to-scroll
display, but you DO get the display.

In these days of cheap RAM, this modification may not have been of so
much use to many people, but it irritated me, so I fixed it.

Added the option (requested by Barry Hall of University of Rochester,
NY) of
treating '~' characters as different to '-' characters. The '~'
character, introduced in GCG9, is for leading and trailing pad
characters. If the option (Shading Prefs) to ignore these pads 
is taken, then they are not counted when the consensus is being
calculated.

E.g. Consider a situation where we have

   ...KG~~~~~~
   ...KGI~~~~~
   ...KG~~~~~~
   ...KGVCNETM
   ...KEVCND~~
   ...K~~~~~~~
at the end of an alignment. Normally, with a 75% threshold value, 
the K residues would be shaded, (6/6) but the Gs would not (4/6). 
If '~' chars are ignored in counting, the G residues are shaded (4/5),
as are the V/Is (3/3) and the pairs of Cs and Ns that follow (2/2 in
each case). Personally, I am not convinced that this is the right 
way to shade the alignment, but I can see that there might be an
arguement for saying that these leading and trailing pads are of a
different nature from internal pads, and should be treated differently.
You have the option.


- Fixes a couple of outstanding bugs:

Program would crash if the last block of sequences was one residue
long, and numbering was turned on;

program would sometimes crash if there was not enough memory to draw
the PICT display;

layout of the identity/similarity matrix wasn't properly aligned in all
cases.


As always, please send any reports of bugs or other problems with
MacBoxshade to:


Michael D. Baron Ph.D.		E-mail: michael.baron at bbsrc.ac.uk
Institute for Animal Health
Ash Road
Pirbright
Surrey GU24 0NF
U.K.




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