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adding a comment about SynView
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Scott Cain committed Nov 14, 2006
1 parent 19df297 commit 9d8bfae
Showing 1 changed file with 7 additions and 1 deletion.
8 changes: 7 additions & 1 deletion docs/pod/CONFIGURE_HOWTO.pod
Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ file should have an entry for it similar to this one:
This indicates that the reference sequence named "Chr1" has length
14972282 bp, method "chromosome" and source "assembly". In addition,
as indicated by the group field, Chr1 has class "Sequence" and name
"Chr".
"Chr1".

It is suggested that you use "Sequence" as the class name for all
reference sequences, since this is the default class used by the
Expand Down Expand Up @@ -1027,6 +1027,12 @@ http://sourceforge.net/mailarchive/message.php?msg_id=12116755 for an
example of using this feature to show assembly gaps as vertical gray
regions.

For a clever example of how to use postgrid calls, see the SynView
synteny browser in the contrib directory of the GBrowse distribution.
It uses a standard GBrowse configuration file with postgrid calls to
draw trapezoids between glyphs to show synteny. For an example of
how this looks, see L<http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?start=101357;stop=121356;ref=MAL12;width=800;version=100;label=AnnotatedGenes-SyntenySpansVivaxMC-SyntenyGenesVivaxMC>.

=item * image_padding = 25

=item * pad_left = 50
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