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Old 09-10-2013, 05:58 PM   #1
fanwei
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Question Synteny analysis

Dear all,

Have you ever been involved in synteny analysis? I feel confused about that.
Can i just input a gene sequence to compare synteny? Or I must input the genomic sequence?
And how do you implement synteny analysis ? Can you recommend me some easy ways?

Thank you!
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Old 09-10-2013, 06:46 PM   #2
SNPsaurus
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You might look at this paper, particularly the comparative genomics methods section:
http://www.genetics.org/content/188/4/799.full
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Old 09-11-2013, 04:35 AM   #3
fanwei
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Quote:
Originally Posted by SNPsaurus View Post
You might look at this paper, particularly the comparative genomics methods section:
http://www.genetics.org/content/188/4/799.full
Have you ever done this analysis before? I feel confused.
I want to analyze synteny of a targeted gene between two species. But one of them just has some scaffold sequences (unfinished sequencing).Can it be used to analyze?

Thank you!
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Old 09-11-2013, 02:19 PM   #4
jimmybee
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Quote:
Originally Posted by fanwei View Post
Have you ever done this analysis before? I feel confused.
I want to analyze synteny of a targeted gene between two species. But one of them just has some scaffold sequences (unfinished sequencing).Can it be used to analyze?

Thank you!
Are you looking to just analyse one gene or a gene family? If its one gene then it should be a simple BLAST against scaffold sequences to identify it. If these are unplaced scaffolds that have no chromosome or genotyping information then you're not going to gauge synteny.
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Old 09-11-2013, 05:36 PM   #5
fanwei
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Quote:
Originally Posted by jimmybee View Post
Are you looking to just analyse one gene or a gene family? If its one gene then it should be a simple BLAST against scaffold sequences to identify it. If these are unplaced scaffolds that have no chromosome or genotyping information then you're not going to gauge synteny.
I know! Thank you very much!
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