Annotate peptide sequence with source exon
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Entering edit mode
20 months ago

Hi, I have a transcript:

transcriptID <- "ENST00000275493"

I obtain the peptide sequence for that transcript:

mart <- useMart(host="ensembl.org", 
                biomart="ENSEMBL_MART_ENSEMBL",
                dataset="hsapiens_gene_ensembl")
petide_seq <- getSequence(id = transcriptID, 
                          type = "ensembl_transcript_id", 
                          seqType = "peptide", 
                          mart = mart)

I would then like to annotate the peptide sequence with the source exon for each part such that I end up with a table like:

| Exon_ID | Peptide_Start | Peptide_End |
|---|---|---|
1 | 1 | 20|
2 | 21 | 40|

Etc...

Can someone recommend a way to do this?

Many thanks

protein R biomaRt • 298 views
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