By using Biomart I have been able to extract prosite patterns for a list of genes for a few species.
e.g. for humans, to extract the prosite patterns start for the foxa3 gene, I would use the code:
library(biomaRt)
ensembl[["hsapiens"]] <- useMart("ensembl", "hsapiens_gene_ensembl")
ensembl <- list()
prosite_foxa3_hsapiens <- getBM(attributes = c("ensembl_gene_id",
"scanprosite_start",
"ensembl_transcript_id",
"transcript_biotype"),
filters = "external_gene_name",
values = "foxa3" ,
mart = ensembl[["hsapiens"]])
I wanted to be able to simply change the mart to the appropriate mart for Ciona intestinalis and use the same attributes e.g.
library(biomaRt)
ensembl[["cintestinalis"]] <- useMart("ensembl", "cintestinalis_gene_ensembl")
prosite_foxa-a_cintestinalis <- getBM(attributes = c("ensembl_gene_id",
"scanprosite_start",
"ensembl_transcript_id",
"transcript_biotype"),
filters = "external_gene_name",
values = "foxa-a" ,
mart = ensembl[["cintestinalis"]])
Unfortunately, there isn't a ''prosite pattern start'' attribute when using listAttributes(ensembl[["cintestinalis"]])
for Ciona intestinalis even though these are available on the Ensembl website.
I wondered if there is maybe a workaround for this?