<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="country-region"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="Street"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="address"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Courier;
panose-1:2 7 4 9 2 2 5 2 4 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman";}
pre
{margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:39673695;
mso-list-template-ids:478970216;}
@list l1
{mso-list-id:331110608;
mso-list-type:hybrid;
mso-list-template-ids:-904360470 134676495 134676505 134676507 134676495 134676505 134676507 134676495 134676505 134676507;}
@list l1:level1
{mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level2
{mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level3
{mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level4
{mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level5
{mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level6
{mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level7
{mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level8
{mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l1:level9
{mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
-->
</style>
</head>
<body lang=DE-CH link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>(sorry, forgot the list
on the CC the first time)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Hello Dave,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>thank you very much for
asking back. You’ve got a good tracking system for unanswered questions :-)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>I think I found the
reason yesterday evening and wanted to work out a solution today so that I
could propose something workable before answering to myself on the list. But as
you asked … here’s what I found out and where my thoughts are going to.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>My first guess was that
something with the MySQL adaptor was broken, but after reproducing the Problem
with SQLite I ditched that assumption. I then tried out the Volvox test data
(as I should have done much earlier) and these worked flawlessly in SQLite
(haven’t tried MySQL yet, but I expect it to work there also). This pointed at
the GFF3 itself. Comparing the Volvox GFF3 and the GFF3 created via
bp_genbank2gff3, I stumbled across this comment in the Volvox GFF3:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<pre><font size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt'># The contig establishes coordinates for segment of sequence<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt'># It needs a name so that users can look it up, but it doesn't need an ID<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt'># because it has no children.<o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Indeed, the GFF3 produced
by bp_genbank2gff3 does not have a single “Name=” in it. It has “ID=”, but no
“Name=”. Adding a few “Name=” by hand I could restore functionality for the
entries which then had a name.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Looks like there were changes
in GBrowse2 in the search functionality where the bp_genbank2gff3 script does
not provide data for at the moment.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>How to fix? Well, a
couple of solutions come to my mind, but I do not know which one is “the best”.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<ol style='margin-top:0cm' start=1 type=1>
<li class=MsoNormal style='color:navy;margin-bottom:12.0pt;mso-list:l1 level1 lfo2'><font
size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial'>As immediate fix, I just hacked a sed script which
simply adds a “Name=” to every entry having an “ID=”<br>
<br>
</span></font><font size=1 color=black face="Courier New"><span
lang=EN-GB style='font-size:9.0pt;font-family:"Courier New";color:windowtext'>sed
-e 's/ID=\([^;]*\)/&;Name=\1/' nc_000964.gbk.gff
>nc_000964.gbk.gff.forgb2</span></font><font size=2 face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial'><br>
<br>
This will of course cause problems for GFF files already having “ID=” and
“Name=”, but for files coming from the current bp_genbank2gff3 it seems
OK.<o:p></o:p></span></font></li>
</ol>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>The next two
possibilities are tightly linked to how GBrowse2 performs its searches and how
the authors define search functionality. As I currently don’t know enough of
this, please read the following just as “ideas”:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<ol style='margin-top:0cm' start=2 type=1>
<li class=MsoNormal style='color:navy;mso-list:l1 level1 lfo2'><font size=2
color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:
Arial'>I could imagine that changing “bp_genbank2gff3” itself might be a
good option. Just adapt it to the fact that GBrowse2 wants “Name=” to be
able to search.<o:p></o:p></span></font></li>
<li class=MsoNormal style='color:navy;mso-list:l1 level1 lfo2'><font size=2
color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:
Arial'>Changing the (search) functionality of GBrowse2 might also be
something worthwhile: every time a “Name=” is missing, use “ID=” (if
existing) as substitute. Though this might have side-effects I don’t know
of yet.<o:p></o:p></span></font></li>
</ol>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>What do you think?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'> Bastien<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>PS: while we are at it:
bp_genbank2gff3 replaces a number of characters with encoded strings (e.g.
%3C). GBrowse2 does not decode these back to normal characters.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<p><font size=2 color=navy face="Courier New"><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:navy'>-- </span></font><b><font
color=red><span lang=EN-GB style='color:red;font-weight:bold'><br>
</span></font></b><font size=2 color=navy face="Courier New"><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:navy'>DSM Nutritional
Products AG<br>
R&D Human Nutrition & Health<br>
Bioinformatics - Bldg. 203.4 / 188<br>
<st1:address w:st="on"><st1:Street w:st="on">P.O. Box</st1:Street> 2676</st1:address><br>
CH-4002 <st1:City w:st="on">Basel</st1:City> / <st1:country-region w:st="on"><st1:place
w:st="on">Switzerland</st1:place></st1:country-region><br>
Tel. </span></font><font size=2 color=navy face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:navy'>+41 61 815 8264</span></font><o:p></o:p></p>
</div>
<div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>
gmodhelp@googlemail.com [mailto:gmodhelp@googlemail.com] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Dave Clements, GMOD Help Desk<br>
<b><span style='font-weight:bold'>Sent:</span></b> Mittwoch, 14. Juli 2010
01:15<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Chevreux,
Bastien</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> <st1:PersonName w:st="on">gmod-gbrowse@lists.sourceforge.net</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Gmod-gbrowse]
Entering GenBank / Refseq file: fail to display in GBrowse2</span></font><span
lang=EN-US><o:p></o:p></span></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Bastien,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Did you ever figure out this problem? If not, I'll spend some
time seeing what I can figure out.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Dave C.<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Mon, Jul 5, 2010 at 6:24 AM, <st1:PersonName w:st="on">Chevreux,
Bastien</st1:PersonName> <<a href="mailto:Bastien.Chevreux@dsm.com">Bastien.Chevreux@dsm.com</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=purple>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Hello
there,</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>I’ve
got GBrowse2 (the latest one could get by installing it last Friday) up and
running fine with the demo data. I also got it running with some small own test
data using the MySQL database, but now I’m running into a problem when I try it
with “real” data from the NCBI.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Synopsis:</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>After
having entered Genbank data from NCBI in a MySQL database, display of search
results yields in a blank page in the browser and the following entry in the
Apache error log: </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>
[Mon Jul 05 14:28:55 2010] [error] [client 172.25.140.138] Can't call method
"seq_id" on an undefined value at
/usr/local/lib/perl/5.10.0/Bio/Graphics/Browser2/Render.pm </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>
line 3640., referer: <a
href="http://chkau66uxas150.kau12.dsm-group.com:2014/cgi-bin/gbrowse/bsub1682/"
target="_blank">http://chkau66uxas150.kau12.dsm-group.com:2014/cgi-bin/gbrowse/bsub1682/</a>”</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>How
to reproduce:</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>I
looked up the current “Tutorial” file in the GBrowse installation and used that
as template. Here’s what I did:</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<ol start=1 type=1>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>Download NC_000964 as GenBank
format (including the sequence) from NCBI: <a
href="http://www.ncbi.nlm.nih.gov/nuccore/NC_000964" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/NC_000964</a>
The file should be some 11 to 12 MiB.</span></font><span lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>Transform to GFF3:<br>
</span></font><font size=2 face=Courier><span lang=EN-GB
style='font-size:10.0pt;font-family:Courier'>bp_genbank2gff3 nc_000964.gbk</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>In a file (bla.sql), save<br>
</span></font><font size=2 face=Courier><span lang=EN-GB
style='font-size:10.0pt;font-family:Courier'> drop database if exists
gb2db_bs1682;<br>
create database gb2db_bs1682;<br>
grant all privileges on gb2db_bs1682.* to gbrowse2@localhost;<br>
grant select on gb2db_bs1682.* to nobody@localhost;<br>
quit</span></font><span lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>Then create MySQL database:</span></font><font
size=2 face=Courier><span lang=EN-GB style='font-size:10.0pt;font-family:
Courier'><br>
mysql -uroot -p <bla.sql</span></font><span lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>Enter GFF3 file into MySQL
database:</span></font><font size=2 face=Courier><span lang=EN-GB
style='font-size:10.0pt;font-family:Courier'><br>
bp_seqfeature_load -c -u gbrowse2 -p ... -a DBI::mysql -d
gb2db_bs1682 nc_000964.fasta nc_000964.gbk.gff</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>In /etc/gbrowse2/GBrowse.conf,
add:<br>
</span></font><font size=2 face=Courier><span lang=EN-GB style='font-size:
10.0pt;font-family:Courier'> [bsub1682]<br>
description = Bacillus subtilis 168<br>
path =
bsub1682.conf</span></font><span lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>In /etc/gbrowse2/bsub1682.conf:<br>
</span></font><font size=2 face=Courier><span lang=EN-GB style='font-size:
10.0pt;font-family:Courier'> [GENERAL]<br>
description = B. subtilis 168 test in MySQL DB<br>
db_adaptor = Bio::DB::SeqFeature::Store<br>
db_args = -dsn gb2db_bs1682<br>
-user
nobody<br>
-pass
""<br>
</span></font><font size=2><span lang=EN-GB style='font-size:10.0pt'>+ the
usual other configuration for a simle genome browser.</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>Navigate with Browser to the
search page of the new genome, enter a search term (e.g. “hisE”) and
search -> blank page</span></font><span lang=EN-GB> </span><o:p></o:p></li>
</ol>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>I’ll
readily admit that I’m novice regarding GBrowse, the likelihood of having done
something wrong is not 0. E.g., in the above “bp_seqfeature_load” call I did
not add a file with FASTA data as I thought it to be unnecessary (the GFF3
contains everything needed). On the other hand, also uploading a FASTA file
didn’t change anything in the results.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>What
have I been doing wrong, or is this a genuine bug?</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Best,</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>
Bastien</span></font><o:p></o:p></p>
<p><font size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt;
font-family:"Courier New"'>-- </span></font><b><font color=red><span
lang=EN-GB style='color:red;font-weight:bold'><br>
</span></font></b><font size=2 face="Courier New"><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>DSM Nutritional Products AG<br>
R&D Human Nutrition & Health<br>
Bioinformatics - Bldg. 203 / 115<br>
<st1:address w:st="on"><st1:Street w:st="on">P.O. Box</st1:Street> 2676</st1:address><br>
CH-4002 <st1:City w:st="on">Basel</st1:City> / <st1:country-region w:st="on"><st1:place
w:st="on">Switzerland</st1:place></st1:country-region><br>
Tel. +41 61 815 8264</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:11.0pt;font-family:Arial'> </span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal><font size=1 color=gray face=Arial><span style='font-size:
7.5pt;font-family:Arial;color:gray'>DISCLAIMER :<br>
This e-mail is for the intended recipient only<br>
If you have received it by mistake please let us know by reply and then delete
it from your system; access, disclosure, copying, distribution or reliance on
any of it by anyone else is prohibited.<br>
If you as intended recipient have received this e-mail incorrectly, please
notify the sender (via e-mail) immediately.</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
------------------------------------------------------------------------------<br>
This SF.net email is sponsored by Sprint<br>
What will you do first with EVO, the first 4G phone?<br>
Visit <a href="http://sprint.com/first" target="_blank">sprint.com/first</a> --
<a href="http://p.sf.net/sfu/sprint-com-first" target="_blank">http://p.sf.net/sfu/sprint-com-first</a><br>
_______________________________________________<br>
Gmod-gbrowse mailing list<br>
<a href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse"
target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
<br clear=all>
<br>
-- <br>
===> PLEASE KEEP RESPONSES ON THE LIST <===<br>
<a href="http://gmod.org/wiki/GMOD_News">http://gmod.org/wiki/GMOD_News</a><br>
<a href="http://gmod.org/wiki/ISMB_2010">http://gmod.org/wiki/ISMB_2010</a><br>
<a href="http://gmod.org/wiki/Help_Desk_Feedback">http://gmod.org/wiki/Help_Desk_Feedback</a><o:p></o:p></span></font></p>
</div>
</div>
</div>
</body>
</html>