Complete CDS of suid herpesvirus - (Apr/21/2014 )

Hi,

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

Thanks.

just on ncbi...

for example: http://www.ncbi.nlm.nih.gov/nucleotide/544169499?report=genbank&log$=nuclalign&blast_rank=56&RID=N9PWAR3301R and than left top corner, press fasta and you get this: http://www.ncbi.nlm.nih.gov/nuccore/544169499?report=fasta

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

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

Inbox on Tue Apr 22 04:09:37 2014 said:

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)

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.