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Erroneous residues at the end of peptide sequences #112

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KoppGergely opened this issue Oct 2, 2024 · 0 comments
Open

Erroneous residues at the end of peptide sequences #112

KoppGergely opened this issue Oct 2, 2024 · 0 comments

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@KoppGergely
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I was trying to access the peptide sequences translated from a set of transcripts. After running the query I manually compared referenced a few transcripts with the sequences available on Uniprot. For most of the transcripts, they matched perfectly, but in some cases there was an additional residue at the end of the sequence provided by biomaRt. Could you look into that?

Here is an example:

library(biomaRt)

ids <- c("ENST00000467907" , "ENST00000563651")
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
filters = "ensembl_transcript_id"
attr <- c("ensembl_transcript_id", "uniprot_isoform", "peptide" )

res_pepseq <- getBM(attributes = attr,
      filters = "ensembl_transcript_id",
      values = ids,
      mart = ensembl
      )

## the official uniprot sequences for the transcript peptides:
up_peptides <- c(
"MAQTDKPTCIPPELPKMLKEFAKAAIRVQPQDLIQWAADYFEALSRGETPPVRERSERVALCNRAELTPELLKILHSQVAGRLIIRAEELAQMWKVVNLPTDLFNSVMNVGRFTEEIEWLKFLALACSA",
"MALPTARPLLGSCGTPALGSLLFLLFSLGWVQPSRTLAGETGQEAAPLDGVLANPPNISSLSPRQLLGFPCAEVSGLSTERVRELAVALAQKNVKLSTEQLRCLAHRLSEPPEDLDALPLDLLLFLNPDAFSGPQACTRFFSRITKANVDLLPRGAPERQRLLPAALACWGVRGSLLSEADVRALGGLACDLPGRFVAESAEVLLPRLGIVAAWRQRSSRDPSWRQPERTILRPRFRREVEKTACPSGKKAREIDESLIFYKKWELEACVDAALLATQMDRVNAIPFTYEQLDVLKHKLDELYPQGYPESVIQHLGYLFLKMSPEDIRKWNV"
)

res_pepseq$peptide == up_peptides

[1] FALSE FALSE

Sequences from uniprot are downloaded from:
https://www.uniprot.org/uniprotkb/C9J6H4/entry#sequences
https://www.uniprot.org/uniprotkb/H3BR90/entry#sequences

Versions:
R 4.4.0
biomaRt 2.60.1

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