question about querying a sequence

ropensci / rentrez

talk with NCBI entrez using R

https://docs.ropensci.org/rentrez

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question about querying a sequence #94

Closed yukund closed 7 years ago

yukund commented 7 years ago

Hi rentrez team

I would like to search a sequence via your rentrez tool

I have tried entrez_search with db name and term. However it does not return any results. see details

entrez_search(db="nucleotide", term="ACAACACACACCCACACACACAACACACCAA")
Entrez search result with 0 hits (object contains 0 IDs and no web_history object)
 Search term (as translated):  (ACAACACACACCCACACACACAACACACCAA[All Fields])

Basically, I want to do capture

Any suggestions will be appreciated. Thanks Yanbo

dwinter commented 7 years ago

Hi @yukund , sadly rentrez doesn't work with BLAST.

I'm not sure there is a good package for the NCBI blast API in R. If you are comfortable with python you could try Biopython ( @Biopython), that project has a nice wrapper in Bio.BLAST.NCBIWWW.

yukund commented 7 years ago

sure, thank you , I will have a look at BioPython.