Read location {GeneR}R Documentation

Get annotations of a GeneBank or an EMBL sequence

Description

Extracts by keywords, from a GeneBank or an EMBL sequence entry, annotations from the features field

Usage

readGbkLocation (file, name = NA, from = 1, to = 0, key = "CDS", subkey
                 = "")
readEmblLocation (file, name = NA, from = 1, to = 0, key = "CDS", subkey
                 = "")

Arguments

file

String/scalar, File name of the bank

name

String/scalar, Sequence name (default : first sequence)

from, to

Integer/scalar, Absolute addresses of the begin and the end of the fragment, (1 means the first nucleotide and 0 conventionally the last one; from must not be larger than to)

key

String/scalar,. Feature to retrieve. (ex: GENE, CDS...)

subkey

String/scalar, Label to retrieve (ex: locus\_tag, note, codon\_start...).

Value

A data frame

Author(s)

P.Durosay(C), L.Cottret(R), A. Lucas

See Also

readEmblLocation,readSeq

Examples


## Not run: 
# Get SARS Sequence
seqNcbi("NC_004718",file="NC_004718.gbk",type="G")

# Get CDS Positions

readGbkLocation(file="NC_004718.gbk")

# Get peptides...
readGbkLocation(file="NC_004718.gbk",key="mat_peptide",subkey="product")

## End(Not run)

# The same with EMBL...
#
# Get SARS Sequence

## Not run: 
download.file("http://bioinfo.hku.hk/sars/AY291451.seq",
destfile="AY291451.seq")


# Get CDS Positions
readEmblLocation(file="AY291451.seq")

# Get peptides...
readEmblLocation(file="AY291451.seq",key="mat_peptide",subkey="product")

## End(Not run)


[Package GeneR version 2.24.0 Index]