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Complete CDS of suid herpesvirus


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#1 Inbox

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Posted 20 April 2014 - 09:35 PM

Hi,

   How can I get complete CDS of Suid herpesvirus from NCBI in single fasta file?

Thanks.



#2 pito

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Posted 21 April 2014 - 12:51 AM

just on ncbi...

 

for example: http://www.ncbi.nlm....ort=genbank$=nuclalign&blast_rank=56&RID=N9PWAR3301R and than left top corner, press fasta and you get this: http://www.ncbi.nlm....99?report=fasta

 

(more than 1 genome, so not sure which you want.. just search for those genomes and than select the ones you want...)


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 Inbox

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Posted 21 April 2014 - 08:09 PM

That is complete genome not CDS. we have to look at FTS server of NCBI for CDS.



#4 pito

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Posted 21 April 2014 - 11:23 PM

That is complete genome not CDS. we have to look at FTS server of NCBI for CDS.

does the server give you a CDS for a virus? 

Did you find the link now? I know there is a FTP server for the whole genomes (of human and mouse), but for CDS for a virus too?

 

(btw in the link I gave you there should be an annotation too of the CDS... (although it does indeed give the full genome, but did not know they have this cds for a virus too)


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#5 phage434

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Posted 22 April 2014 - 04:55 AM

If the CDS is annotated in the Genbank entry, then clicking on the "CDS" label will subset the sequence to just the sequence of the CDS. You can then switch to FASTA as above. If the CDS is not annotated, then ORFFINDER will help you isolate it.






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