Finding contig or scaffold location in GBrowse

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Finding contig or scaffold location in GBrowse

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



 

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Re: Finding contig or scaffold location in GBrowse

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 form:


Good luck,
Scott


On Thu, Feb 19, 2015 at 9:42 PM, Simon Deroles <[hidden email]> wrote:
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: <a href="tel:%2B64%206%20355%206112" value="+6463556112" target="_blank">+64 6 355 6112
F: <a href="tel:%2B64%206%20351%207050" value="+6463517050" target="_blank">+64 6 351 7050
[hidden email]
www.plantandfood.co.nz
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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Re: Finding contig or scaffold location in GBrowse

Alexey Morozov
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.

2015-02-20 23:53 GMT+08:00 Scott Cain <[hidden email]>:
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:


Good luck,
Scott


On Thu, Feb 19, 2015 at 9:42 PM, Simon Deroles <[hidden email]> wrote:
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: <a href="tel:%2B64%206%20355%206112" value="+6463556112" target="_blank">+64 6 355 6112
F: <a href="tel:%2B64%206%20351%207050" value="+6463517050" target="_blank">+64 6 351 7050
[hidden email]
www.plantandfood.co.nz
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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--
------------------------------------------------------------------------
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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--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

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