extract_5ss_motif: Extract the donor splice site motif for MaxEntScan web tool

In monahton/GencoDymo: Data Extraction and Manipulation from the GENCODE Database

Extract the donor splice site motif for MaxEntScan web tool

Description

This function takes a dataframe of intron coordinates and the full genome sequence of a particular species and return a "bed-file" structured data frame containing the motif coordinates, their corresponding transcripts id and intron number, and the motif sequence which are also saved as a fasta file in the working directory. The fasta file can be uploaded to MaxEntScan::5ss web tool for the retrieval of the scores of acceptor splice sites.

Usage

extract_5ss_motif(input,genome)

Arguments

input	The name of the data frame containing intron coordinates
genome	The full genome sequence of a particular species. The default value is the human genome sequence of the hg38 assembly

Value

A data frame with motif coordinates and their sequences

See Also

extract_3ss_motif

Examples

extract_5ss_motif(introns_df, genome=BSgenome.Hsapiens.UCSC.hg38)

monahton/GencoDymo documentation built on Dec. 13, 2024, 1:23 a.m.