rfamSeedAlignment: Retrieve the seed alignment of an Rfam family

In rfaRm: An R interface to the Rfam database

Description

Retrieves the seed multiple alignment of the specified Rfam family. The seed alignment is used to determine the covariance model defining each Rfam family, and comprises only a subset of all the members of each family. If a filename is provided, the alignment will be saved in the specified format.

Usage

rfamSeedAlignment(rfamFamily, filename=NULL, format="stockholm")

Arguments

rfamFamily	string with an Rfam family accession or ID for which the seed alignment should be retrieved.
filename	string indicating a path to which the retrieved seed alignment should be written. The format of the written file is determined by the "format" argument. In the default behaviour, filename=NULL, and no file will be written. Instead, the seed alignment will just be returned as a Biostrings MultipleAlignment object.
format	string indicating the format into which the seed alignment should be retrieved and written to filename Can be one of "stockholm" (default), "pfam", "fasta" or "fastau". For a description of each type of format, see https://docs.rfam.org/en/latest/api.html#stockholm-format-alignment.

Value

A Biostrings MultipleAlignment object with the aligned RNA sequences included in the seed alignment. The names of the sequences contain their GenBank accession numbers and the start and end positions of the region corresponding to the sequence region member of the Rfam family.

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 Biostrings MultipleAlignment object with the aligned RNA sequences
# used to generate the seed alignment for the Rfam family with ID "FMN"

rfamSeedAlignment("FMN")

# Generate a Biostrings MultipleAlignment object with the aligned RNA sequences
# used to generate the seed alignment for the Rfam family with accession
# "RF00174", and save it to a file in Stockholm format

rfamSeedAlignment("RF00174", filename="RF00174seedAlignment.stk", format="stockholm")

# Generate a Biostrings MultipleAlignment object with the aligned RNA sequences
# used to generate the seed alignment for the Rfam family with accession
# "RF00174", and save it to a file in FASTA format

rfamSeedAlignment("RF00174", filename="RF00174seedAlignment.fasta", format="fasta")

rfaRm documentation built on March 16, 2021, 6:01 p.m.