NCBI BLAST output format

Brian Foley brianf at med.uvm.edu
Thu Jan 6 20:15:51 EST 1994

Bill Kupiec (kupiec at mail1.ciwemb.edu) wrote:
: RE>NCBI BLAST output format: Q
: Brian,

: > Can someone tell me what is the best software for viewing the
: > output from an NCBI BLAST search?  Whether I read the output in
: > my UNIX e-mail, my Mac e-mail, or convert it to a text editor
: > (MS-Word) document, the alignments do not line up without
: > messing with them.

: In your text editor (MS-Word, WordPerfect), change the font to a mono-spaced
: typeface such as Courier or Monaco and the alignments should line up 
: perfectly.

	It's not just the alignments but also the histogram and other
output.  And it still looks bad even in courier font.

: -Bill
: *------------------------------------------------------------*
: Bill Kupiec
: kupiec at mail1.ciwemb.edu, AppleLink: KUPIEC
: Operations Manager, Carnegie Institution of Washington
: *------------------------------------------------------------*

	I should have mentioned that I was using courier font.  It
still does not line up.  And when I start pushing a line over by
adding spaces at the left edge, not all characters on the line
move together.  A few just to the right of the cursor shift, then
the rest of the line might jump over by five spaces as the next space
is added, while those characters just to the right of the cursor only
move by the expected one space.  To me it looks like some of the
spacing is done with TABs.  This would cause such behavior.
	Apparently, I am the only one having such difficulties,
so it must be specific to the Mac and MS-Word text editor I am
using.  I will try something different now, and see if that
fixes everything.  Several people wrote to me personally
and assured me that the BLAST output does look nicely formatted
on their systems.
	Thanks for all the responses.

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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