[Gmod-gbrowse] Finding contig or scaffold location in GBrowse

Discussion:

Simon Deroles

2015-02-20 02:42:59 UTC

Hi There

Please forgive me if this is a stupid question. I am looking at the Kiwifruit genome database at http://bioinfo.bti.cornell.edu/cgi-bin/kiwi/home.cgi.

I have used BLAST to find a seq of interest and it is able to locate the seq on either a scaffold location or config location. I now want to look at the flanking regions around this seq but am unable to use the scaffold or config indentifiers to go to their location in Gbrowse. How do i find the reverent region in Gbrowse? The BLAST results do not return a gene name or chromosome location.

Many thanks for your help

Kind Regards

Simon Deroles
Simon Deroles
Senior Scientist

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Scott Cain

2015-02-20 15:53:43 UTC

Permalink

Hi Simon,

This is the mailing list for supporting people who install the software
that powers the Kiwi genome browser, GBrowse. Unfortunately, I don't know
anything about the specifics of the data they have in their instance of
GBrowse, nor how it relates to data they've made available through their
blast interface. I suggest you contact them directly with their contact
form:

http://bioinfo.bti.cornell.edu/cgi-bin/kiwi/contact.cgi

Good luck,
Scott

On Thu, Feb 19, 2015 at 9:42 PM, Simon Deroles <

Post by Simon Deroles
Hi There
Please forgive me if this is a stupid question. I am looking at the
Kiwifruit genome database at
http://bioinfo.bti.cornell.edu/cgi-bin/kiwi/home.cgi.
I have used BLAST to find a seq of interest and it is able to locate the
seq on either a scaffold location or config location. I now want to look
at the flanking regions around this seq but am unable to use the scaffold
or config indentifiers to go to their location in Gbrowse. How do i find
the reverent region in Gbrowse? The BLAST results do not return a gene
name or chromosome location.
Many thanks for your help
Kind Regards
Simon Deroles
*Simon Deroles*Senior Scientist
T: +64 6 355 6112
F: +64 6 351 7050
The New Zealand Institute for Plant & Food Research Limited
*Postal Address:* Plant & Food Research Palmerston North
Private Bag 11600, Manawatu Mail Centre, Palmerston North, 4442, New Zealand
*Physical Address:* Plant & Food Research Palmerston North
Batchelar Road, Palmerston North, 4474, New Zealand
The contents of this e-mail are confidential and may be subject to legal privilege.
If you are not the intended recipient you must not use, disseminate, distribute or
reproduce all or any part of this e-mail or attachments. If you have received this
e-mail in error, please notify the sender and delete all material pertaining to this
e-mail. Any opinion or views expressed in this e-mail are those of the individual
sender and may not represent those of The New Zealand Institute for Plant and
Food Research Limited.
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Alexey Morozov

2015-02-25 15:49:24 UTC

Permalink

There is this yellow "Show this or that much bp/kbp/Mbp" thingie on the
top-right. Scroll out with +- buttons or edit "Landmark or region"
coordinates manually.

Post by Scott Cain
Hi Simon,
This is the mailing list for supporting people who install the software
that powers the Kiwi genome browser, GBrowse. Unfortunately, I don't know
anything about the specifics of the data they have in their instance of
GBrowse, nor how it relates to data they've made available through their
blast interface. I suggest you contact them directly with their contact
http://bioinfo.bti.cornell.edu/cgi-bin/kiwi/contact.cgi
Good luck,
Scott
On Thu, Feb 19, 2015 at 9:42 PM, Simon Deroles <

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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