genome sequences location

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genome sequences location

殷冬梅

Dear Dr. ,
I am glad to hear from you. Now we have got some trouble in Blat alignment.
Such as, I want to know the location of a sequence , enter the seq., then find more locations.

<img width="54" height="124" src="data:image/png;base64,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" v:shapes="_x0000_i1025">         <img width="62" height="108" src="data:image/png;base64,R0lGODdhPgBsAHcAACH+GlNvZnR3YXJlOiBNaWNyb3NvZnQgT2ZmaWNlACwAAAAAPgBsAIEAAADT09P/AAD//wAC/4yPmcDdCqOcNLCB82C1e3ppGveVZSiOgMlWQAqviUDX7QmnMlLbQU+7KVA5DIkCFAgXRd3y+WqOnsuo1EgVWq+7rGkr7Xo/4KZ43CkXz2jQNcNuS9S5uBxCj909eefe9Yb15xZoN2jQJ2J4mDh1OBe48QhZOBnRCGeJF7k4iCmoifApGSrKWWpaiYp4umrRujra+Sfr+qoaC4ta68qbi7urW+obDDwsHEp8bJyMrKnczPzsbAk9LV1NPWmdjb2t/cj97R0OzmjuiU6rvideTn4Ony6/Tt/Ofuce/zZ7b5+PT46+efxsDaxXsFfANgf9Jfz1sFjEZROjVbx2sVvGcT8b33Xcx8XgQjQNAf4TOHJMSZQnGab0stJlS5Ivs8SkOVNlTSo3VWI6sutnP4dmbCFKBLRXnqQG1TA16iDqnwIAOw==" v:shapes="_x0000_i1026">      <img width="54" height="57" src="data:image/png;base64,R0lGODdhNgA5AHcAACH+GlNvZnR3YXJlOiBNaWNyb3NvZnQgT2ZmaWNlACwAAAAANgA5AIEAAADT09P/AAD//wACwIyPmcDdCqOciI2LB6O8K5tlm0dOYCgC5fqhrsrGAeCisFye9TXiHr0L3XwcYBAzJJqOImXHyEw6IdCjdLpgIrFLrYYrqQav4Jn3W255yWDxjs111+BY+Sut1tKndhs+u/ZXcbbn1CckeHDYlGgW2Li4BUnY6KhXGcmDSTn5mJiJ9skp6ikIWqh0uln6p9p5+Rq1CktKazp6y4rnWisbazXr+xnZY0qMmmo7bIVsaFdcOeMGfSBgfV3moC1xjS1RAAA7" v:shapes="_x0000_i1027">       <img width="54" height="140" src="data:image/png;base64,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" v:shapes="_x0000_i1028">

 Aradu.A01   Aradu.A02   Aradu.A08   Aradu.A09

 

Name

Type

Description

Position

積分=%s

Alignment1

BLAT

 

Aradu.A01:92825185..92826133

44.80

Alignment2

BLAT

 

Aradu.A08:47742102..47743317

42.01

Alignment3

BLAT

 

Aradu.A02:3894758..3895967

41.33

Alignment4

BLAT

 

Aradu.A02:3927022..3928239

40.57

Alignment5

BLAT

 

Aradu.A09:106585367..106585834

35.22

 

How to make sure its location? And why?

Thank you very much.

Dongmei




祝工作顺利!

 Dongmei Yin (Ph.D)

        The college of Agronomy,

         Henan Agricultural University,       

         Zhengzhou, Henan, 450002




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Re: genome sequences location

Scott Cain
Hello Dongmei,

You've reached the mailing list for supporting people who install GBrowse software. I think you're asking about the data that somebody else loaded into gbrowse and made available to the general public. Your best bet for getting help is to find the owner of the website and ask them. If you can't figure out who that is, you can ask here, as we know lots of people in various communities. 

Good luck,
Scott


Sent from my iPhone

On Jul 30, 2014, at 5:41 PM, 殷冬梅 <[hidden email]> wrote:


Dear Dr. ,
I am glad to hear from you. Now we have got some trouble in Blat alignment.
Such as, I want to know the location of a sequence , enter the seq., then find more locations.

<img width="54" height="124" src="data:image/png;base64,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" v:shapes="_x0000_i1025">         <img width="62" height="108" src="data:image/png;base64,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" v:shapes="_x0000_i1026">      <img width="54" height="57" src="data:image/png;base64,R0lGODdhNgA5AHcAACH+GlNvZnR3YXJlOiBNaWNyb3NvZnQgT2ZmaWNlACwAAAAANgA5AIEAAADT09P/AAD//wACwIyPmcDdCqOciI2LB6O8K5tlm0dOYCgC5fqhrsrGAeCisFye9TXiHr0L3XwcYBAzJJqOImXHyEw6IdCjdLpgIrFLrYYrqQav4Jn3W255yWDxjs111+BY+Sut1tKndhs+u/ZXcbbn1CckeHDYlGgW2Li4BUnY6KhXGcmDSTn5mJiJ9skp6ikIWqh0uln6p9p5+Rq1CktKazp6y4rnWisbazXr+xnZY0qMmmo7bIVsaFdcOeMGfSBgfV3moC1xjS1RAAA7" v:shapes="_x0000_i1027">       <img width="54" height="140" src="data:image/png;base64,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" v:shapes="_x0000_i1028">

 Aradu.A01   Aradu.A02   Aradu.A08   Aradu.A09

 

Name

Type

Description

Position

積分=%s

Alignment1

BLAT

 

Aradu.A01:92825185..92826133

44.80

Alignment2

BLAT

 

Aradu.A08:47742102..47743317

42.01

Alignment3

BLAT

 

Aradu.A02:3894758..3895967

41.33

Alignment4

BLAT

 

Aradu.A02:3927022..3928239

40.57

Alignment5

BLAT

 

Aradu.A09:106585367..106585834

35.22

 

How to make sure its location? And why?

Thank you very much.

Dongmei




祝工作顺利!

 Dongmei Yin (Ph.D)

        The college of Agronomy,

         Henan Agricultural University,       

         Zhengzhou, Henan, 450002



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Re: genome sequences location

Nathan Weeks
In reply to this post by 殷冬梅
Hi Dongmei,

The locations of the sequence you aligned are of the form
chromosome:start..end; e.g., the best match aligned to
Aradu.A01:92825185..92826133, which indicates chromosome Aradu.A01
between from 92825185 to 92826133.

Clicking on this alignment takes you to that region in GBrowse; from
there, you can click on the alignment (in the BLAT track) to see the
underlying sequence.

The score (44.80, 42.01. etc) in the results list essentially the %
query coverage (defined as (matches+mismatches)/query_length), so the
listed alignments cover from over 1/3 to less than 1/2 of the query
sequence matched. If you're aligning a sequence from another species,
the default 90% identity may be a bit stringent; for our next
first-Tuesday-of-the-month release (August 5th) of PeanutBase, we're
adding the ability for the user to specify the percent identity in the
BLAT plugin (described here: https://github.com/GMOD/GBrowse/pull/43)

Further questions specific to PeanutBase can be submitted using the
"contact us" form here:

http://peanutbase.org/contact

Regards,

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
Crop Genome Informatics Laboratory
Iowa State University
http://weeks.public.iastate.edu/

On Thu, Jul 31, 2014 at 11:00 AM,
<[hidden email]> wrote:

> Message: 4
> Date: Thu, 31 Jul 2014 05:41:11 +0800 (CST)
> From: ??? <[hidden email]>
> Subject: [Gmod-gbrowse] genome sequences location
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="gbk"
>
>
>
> Dear Dr. ,
> I am glad to hear from you. Now we have got some trouble in Blat alignment.
> Such as, I want to know the location of a sequence , enter the seq., then find more locations.
>
>
>
>
>
>  Aradu.A01   Aradu.A02   Aradu.A08   Aradu.A09
>
>
>
> |
>
> Name
>
> |
>
> Type
>
> |
>
> Description
>
> |
>
> Position
>
> |
>
> ??=%s
>
> |
> |
>
> Alignment1
>
> |
>
> BLAT
>
> |
>
>
>
> |
>
> Aradu.A01:92825185..92826133
>
> |
>
> 44.80
>
> |
> |
>
> Alignment2
>
> |
>
> BLAT
>
> |
>
>
>
> |
>
> Aradu.A08:47742102..47743317
>
> |
>
> 42.01
>
> |
> |
>
> Alignment3
>
> |
>
> BLAT
>
> |
>
>
>
> |
>
> Aradu.A02:3894758..3895967
>
> |
>
> 41.33
>
> |
> |
>
> Alignment4
>
> |
>
> BLAT
>
> |
>
>
>
> |
>
> Aradu.A02:3927022..3928239
>
> |
>
> 40.57
>
> |
> |
>
> Alignment5
>
> |
>
> BLAT
>
> |
>
>
>
> |
>
> Aradu.A09:106585367..106585834
>
> |
>
> 35.22
>
> |
>
>
>
> How to make sure its location? And why?
>
> Thank you very much.
>
> Dongmei
>
>
>
>
>
>
>
> ??????
>
>  Dongmei Yin (Ph.D)
>
>         The college of Agronomy,
>
>          Henan Agricultural University,
>
>          Zhengzhou, Henan, 450002

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