[Bioperl-l] GBroswe2 - feature details

[Alper Yilmaz]

Dear all,

I have a question about utilizing the tag/value pairs that were used
in 9th of GFF. If my 9th column is like this:

ID=BS_1;BS_Seq=cacatg;BS_Color=Purple;Name=AtMYC2 BS in RD22

How can I use BS_Seq, BS_Color tags, say, in a balloon? If want to
print name and sequence of a BindingSite, what do I need to replace
question marks below?

balloon hover = <font size=small color=red>Motif name: $name,
Sequence: ???????</font>


The manual is mentioning that it's possible to use user defined
tag/value pairs, but I couldn't figure out how. The manual is
mentioning:
 [feature_type:details]
 tag1 = formatting rule
 tag2 = formatting rule
 tag3 = formatting rule

can be used to adjust formatting of a tag, but I don't how this can be
used to assign value to a tag? I tried ;
[cis-elements:details]
bs_seq = <b>$value</b>     (I didn't use BS_Seq, since it was
mentioned, tags are case-insensitive)
 OR
$bs_seq = <b>$value</b>

but, I cannot use $bs_seq in hover link option after doing this. What
am I doing wrong?

thanks,

Alper Yilmaz
Post-doctoral Researcher
Plant Biotechnology Center
The Ohio State University
1060 Carmack Rd
Columbus, OH 43210
(614)688-4954
www.grassius.org