[Bioperl-l] GBroswe2 - feature details

Alper Yilmaz alperyilmaz at gmail.com
Fri Jun 5 14:50:46 EDT 2009

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
 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 ;
bs_seq = <b>$value</b>     (I didn't use BS_Seq, since it was
mentioned, tags are case-insensitive)
$bs_seq = <b>$value</b>

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


Alper Yilmaz
Post-doctoral Researcher
Plant Biotechnology Center
The Ohio State University
1060 Carmack Rd
Columbus, OH 43210

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