library(biomaRt)
biomart <- "plants_mart"
dataset <- "athaliana_eg_gene"
mart <- useMart(biomart = biomart, dataset = dataset)
protein_ids <- c("AT5G67220.1", "AT1G07110.1", "AT5G39570.1")
protein_sequences <- getSequence(id = protein_ids, type = "ensembl_gene_id", seqType = "protein", mart = mart)
protein_data <- data.frame(Protein_ID = protein_ids, Protein_Sequence = protein_sequences, stringsAsFactors = FALSE)
output_file <- "protein_data.xlsx"
write.xlsx(protein_data, output_file)
> listMarts(host="https://plants.ensembl.org")
biomart version
1 plants_mart Ensembl Plants Genes 57
2 plants_variations Ensembl Plants Variations 57
I used the following listmarts to check the biomart and what I have used is correct, however, I am keep getting the below error message.
Error in .useMart(biomart, dataset, host = host, path = path, port = port, : Incorrect BioMart name, use the listMarts function to see which BioMart databases are available