Question: Ensembl REST requests for CDS sequences returning AA sequences
0
gravatar for heath.obrien
4.3 years ago by
United Kingdom
heath.obrien0 wrote:

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 • 1.3k views
ADD COMMENTlink modified 4.3 years ago by Tariq Daouda210 • written 4.3 years ago by heath.obrien0

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

ADD REPLYlink written 4.3 years ago by Emily_Ensembl18k
4
gravatar for ayates
4.3 years ago by
ayates60
United Kingdom
ayates60 wrote:

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.

ADD COMMENTlink written 4.3 years ago by ayates60

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

ADD REPLYlink written 4.3 years ago by heath.obrien0
0
gravatar for Tariq Daouda
4.3 years ago by
Tariq Daouda210
IRIC | Institute for Research in Immunology and Cancer
Tariq Daouda210 wrote:

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

ADD COMMENTlink written 4.3 years ago by Tariq Daouda210
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