seqinr: gbk2g2.euk – R documentation

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gbk2g2.euk

Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version.

Description

This function reads a file in GenBank format and converts the features corresponding to CDS (Coding Sequences) into a format similar to glimmer program output. This function is specifically made for eukaryotic sequences, i.e. with introns.

Usage

gbk2g2.euk(gbkfile = system.file("sequences/ame1.gbk", package ="seqinr"),
g2.coord = "g2.coord")

Arguments

`gbkfile`	The name of the GenBank file
`g2.coord`	The name of the output file

Details

This function returns the coordinates of the exons annotated in the GenBank format file.

Value

A data frame with three columns will be written to the g2.coord file. The first column corresponds to the name of the gene, given in the GenBank file through the /gene feature. The second and third column contain the start and the stop position of the exon.

Author(s)

J.R. Lobry, A. Necşulea

References

citation("seqinr")

Examples

## Not run:  gbk2g2.euk()

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19