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Ensembl REST requests for CDS sequences returning AA sequences

Hi,

I'm trying to use the Ensembl REST API to retrieve CDS sequences which works great most of the time, but occasionally it returns an amino acid sequence instead. Here's an example:

guest-028-002-021: User$ curl 'http://rest.ensemblgenomes.org/sequence/id/GLYMA13G38430.1?content-type=text/x-fasta;type=cds'
>GLYMA13G38430.1
MPAGIMIPARNMPSMIGRNGTVGGFGLSSGLSLGQIENHKASESQRSEEMFQPNLMEAGQ
LHPLDMPQNTSESDVPRIREDDFDSATKSGSENLEGASGEDQDPRPNKKKRYHRHTQHQI
QEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHERHENTQLRTENE
KLRADNMRFREALGNASCPNCGGPTAIGEMSFDEHHLRLENARLREEIDRISAIAAKYVG
KPVVSYPLVSPSSIPPRPLELGIGGGFGGQPGGTGGDMYGGAAGDLLRSISGPTEADKPI
IIELAVAAMEELIGMAQMGEPLWLTTLDGTTVLNEDEYIRSFPRGIGPKPAGFKFEASRE
TAVVIMNHVNLVEILMDVNQWSTVFAGIVSRAMTLEVLSTGVAGNYNGALQVMTAEVQVP
SPLVPTRESYFVRYCKQHGDGTWAVVDVSLDNLRPSPSARCRRRPSGCLIQEMPNGYSKV
IWVEHVEVDDRGVHNLYKQLVSSGHAFGAKRWVATLDRQCERLASAMATNIPTVDVGVIT
NQDGRKSMLKLAERMVISFCAGVSASTAHTWTTLSGTGADDVRVMTRKSVDDPGRPPGIV
LSAATSFWLPVSPKRVFEFLRDENSRSEWDILSNGGVVQEMAHIANGRDTGNCVSLLRVN
SANSSQSNMLILQESCADSTGSFVIYAPVDIVAMNVVLNGGDPDYVALLPSGFAILPDGT
TAHGGGIGDTGHGGSLLTVAFQILVDSVPTAKLSLGSVATVNNLIACTVERIKAALSGEV
A

Am I doing something wrong? GLYMA13G38430.1 is a valid TranscriptID when I look it up on the Ensembl Genomes website. I'm stumped. I'd appreciate any suggestions that folks might have. Thanks!

cds ensembl rest
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updated by Ram Ram • written by heath.obrien • heath.obrien

Not sure at the moment. Fairly sure it's not you. In touch with our developers to find out.

• 1 views • link
written by Emily Emily

2 answers

Ok so this is caused by the reuse of stable identifiers between the different object types we have. GLYMA13G38430.1 is reused for both the transcript and translation stable identifier. The underlying Perl API is struggling to know which one you're requesting. You can get around this by forcing it to look for transcripts which will give you the CDS:

curl 'http://rest.ensemblgenomes.org/sequence/id/GLYMA13G38430.1?content-type=text/x-fasta;type=cds;object_type=transcript'

Hope this helps and sorry for the confusion.

• 1 views • link
updated by Ram Ram • written by ayates ayates

Great. That seems to be working perfectly. Thanks a lot.

• 0 views • link
written by heath.obrien • heath.obrien

If you have many sequences to fetch and don't mind a little python, pyGeno could also be good alternative.

• 1 views • link
written by Tariq Daouda Tariq Daouda

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