blast - how to find homologs of a protein int the given list of taxonomies

Question

[maahpishanu]

Hello,

I have the following blast code which works properly:

> s
[1] "O48946"
system2('blastp',c('-db','refseq_protein','-remote'
, '-entrez_query'
, 'txid15368[ORGN]'
, '-outfmt',sprintf('"6 %s"',paste(collapse=' ',blast.f6))
)
,input= s
,stdout=TRUE
)

Now I would like to add another species to my taxonomy database. I learned that this is possible if I write:

'( txid15368[ORGN] AND txid3847[ORGN]) )'

but this is not working at all and produces the following error:

Error: Too many positional arguments (1), the offending value: AND

Also I would like to exclude a taxonomy from my blastp for which I learned that the following line should do it:

'( txid15368[ORGN] AND txid3847[ORGN]) ) NOT (txid3702[ORGN])'

still I get the same error:

Error: Too many positional arguments (1), the offending value: AND

I would appreciate a lot your help.

Best
Maah

[Michael]

'( txid15368[ORGN] AND txid3847[ORGN] ) )' you have an unmatched parenthesis