seqSrs {GeneR}R Documentation

Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs

Description

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).

Usage

seqSrs (accno,file="toto.seq",submotif=FALSE,
srs="http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz",
bank=c("EMBL","REFSEQ"))
seqNcbi (accno,file="toto.seq",submotif=FALSE,type="fasta")

Arguments

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

type

fasta or genbank for seqNcbi (file format of sequence).

bank

List of banks to search into.

Value

1 if file has been correctly created. A file containing the sequence in file format requested

Note

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).

Author(s)

Antoine Lucas, Centre de Genetique moleculaire, CNRS Gif / Yvette

Examples

seqNcbi("BY608190",file="BY608190.fa")


## Not run: 
# idem:
seqSrs("dbj|BY608190.1|BY608190",file="BY608190.embl",submotif=TRUE,type="embl")

seqSrs("AK129232",type="embl",srs="http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz")

## End(Not run)
  

[Package GeneR version 2.24.0 Index]