[Seqinr-forum] Problem with query when species are not in Genbank

[Maxime Réjou-Méchain]

Dear all,

I am currently using a loop with the function query to know which genera in
my list (n>2000 genera) have some sequences in genbank.

Here is the loop:

choosebank("genbank")
sequences=vector(mode="numeric",length=length(Genustobefind))
for (i in 1:length(Genustobefind)){
print(paste("Retrieving sequence ",Genustobefind[i]," i=",i,sep=""))
query1=paste("SP=",Genustobefind[i], " AND K=rbcl", sep="")
query("bb", query1,virtual=T)
sequences[i]=bb$nelem
}

The loop work well but a lot of genera block the query function. For
example, if I do

query("bb", "SP=Acanthodium AND K=rbcl",virtual=T)

The function run without stopping. I thus have to break the loop.

For information, if I submit manually the genera that block the query
function to genbank I obtain in the main cases:

   - The following term was not found in Nucleotide: Acanthodium.
   - See the search
details<http://www.ncbi.nlm.nih.gov/nuccore/details?querykey=1>.

   - No items found.

In fact all these genera are not present in Genbank. Have you any idea to
overcome this problem? I just want to have a value of zero for these genera
and to continue my loop.
Many thanks in advance for your help,

Maxime
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