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Old 12-18-2013, 09:42 PM   #1
roshanbernard
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Default Help with annotations

Hi,

I have WGS of Bacteria.

However when i cross checked the annotation done by RAST-SEED server.

i can see some errors.

Same nucleotides have been given different annotation names.

Can someone tell me why is this happening.

Regards

rosh
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Old 12-18-2013, 11:19 PM   #2
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Maybe you could clarify a little bit..
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Old 12-19-2013, 03:58 AM   #3
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Thanks for your reply...

when i checked the WGS and there is a gene which is 903bp on two different contigs of same genome. But the annotations are given below for each

2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) CDS

D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) CDS

i am pretty confused why is this giving the data like this


thanks in advance

regards
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Old 12-19-2013, 04:40 AM   #4
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Quote:
Originally Posted by roshanbernard View Post
there is a gene which is 903bp on two different contigs of same genome
What do you mean? The same exact 903bp sequence can be found from two different contigs and then RAST-SEED says that the other one gives a hit to 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) CDS and the other one to D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) CDS?
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Old 12-19-2013, 04:44 PM   #5
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Yeah exactly.... its the same 903bp... same nucleotides but the annotation is different... so i am wondering...

thanks
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Old 12-19-2013, 10:58 PM   #6
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So it's not giving the same two hits for both sequences?
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Old 12-19-2013, 10:59 PM   #7
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Yes exactly... thats the problem.. i dont know why this is happening..
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Old 12-19-2013, 11:04 PM   #8
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Quote:
Originally Posted by roshanbernard View Post
Yes exactly... thats the problem.. i dont know why this is happening..
Proteins are usually made up of multiple domains, and these domains show up in 1000s of different proteins. So perhaps that's what you're seeing? You're getting a weak secondary hit to some non orthologous protein..
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