rfamSequenceRegions: Retrieve all sequence regions belonging to an Rfam family

In LaraSellesVidal/rfaRm: An R interface to the Rfam database

Description

Retrieves all sequence regions encoding an RNA assigned to be a member of the specified Rfam family. If a filename is provided, the list of sequence regions will be saved to the path specified through filename as a tab-delimited file.

Usage

rfamSequenceRegions(rfamFamily, filename=NULL)

Arguments

rfamFamily	string with an Rfam family accession or ID for which the member sequence regions should be retrieved.
filename	string indicating a path to which the retrieved sequence regions should be written as a tab-delimited file. In the default behaviour, filename=NULL, and no file will be written. Instead, the sequence regions will be returned as a data frame.

Value

A data frame with the sequence regions belonging to the specified Rfam family. The data frame contains the following columns:

Sequence GenBank accession	GenBank accession of the sequence with the sequence region belonging to the Rfam family
Bit score	Bit score for the alignment of the sequence region to the Rfam family
Region start position	Position of the sequence specified by the GenBank accession where the sequence region belonging to the Rfam family starts
Region end position	Position of the sequence specified by the GenBank accession where the sequence region belonging to the Rfam family ends
Sequence description	Description of the sequence where the sequence region belonging to the Rfam family is found
Species	Name of the species where the sequence region is present
NCBI tax ID	NCBI taxonomy ID of the species where the sequence region is present

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

# Generate a data frame with the sequence regions belonging to the Rfam family
# with ID "FMN"

head(rfamSequenceRegions("FMN"))

# Generate a data frame with the sequence regions belonging to the Rfam family
# with accession "RF00360", and save the sequence regions as a tab-delimited
# text file.

head(rfamSequenceRegions("RF00360", filename="RF00360sequenceRegions.txt"))
## Not run: 
# Some Rfam families have too many associated sequence regions, in which case
# the list cannot be retrieved from the server.

rfamSequenceRegions("RF00174")

## End(Not run)

LaraSellesVidal/rfaRm documentation built on Aug. 8, 2021, 7:25 p.m.