SeqUrl {GeneR} | R Documentation |
Get a sequence in Fasta / Genbank / Embl format trough web with only an accno
seqUrl will get the sequence through a srs web program. seqNcbi will do the same with ncbi web server (I prefer this one).
seqUrl (accno,file="toto.seq",submotif=FALSE, srs="http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz", type="fasta",bank=c("EMBL","REFSEQ"),srsversion=7) seqNcbi (accno,file="toto.seq",submotif=FALSE,type="fasta")
accno |
Access Number: "dbj|BY608190.1|BY608190" or "BY608190" |
file |
file where seqence will be downloaded |
submotif |
a logical value indicating whether we look for a subpatern of accno |
srs |
a url srs web program |
srsversion |
srs web program version |
type |
fasta or genbank for seqNcbi; fasta or embl for seqUrl (file format of sequence). |
bank |
List of banks to search into. |
1 if file has been correctly created. A file containing the sequence in file format requested
SeqNcbi returns sometimes Genbank file in a not very valid format (specially with EST sequences). These files will not be computed by readseq. (Use Fasta format, then).
Antoine Lucas, Centre de Génétique moléculaire, CNRS Gif / Yvette
seqNcbi("BY608190",file="BY608190.fa") ## Not run: # idem: seqUrl("BY608190",file="BY608190.fa") seqUrl("dbj|BY608190.1|BY608190",file="BY608190.embl",submotif=TRUE,type="embl") seqUrl("AK129232",type="embl",srs="http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz") ## End(Not run)