[ensembl-dev] Retrieval of aligned transcripts using API

Tjaart de Beer tjaart at ebi.ac.uk
Tue Feb 22 16:52:35 GMT 2011

Hi all

I would like to know if it is possible to get an aligned set of
transcripts for a specific gene from one species from Ensembl?

E.g. When looking at

we see there are 8 transcripts of which 4 potentially codes for a protein.
Transcripts ENST0000280097, ENST00000410115, ENST00000280096 will all
align without any problem. The problem comes in when adding
ENST00000329366. This transcript contains an exon that none of the other
transcripts do. When using the sequences of the 4 transcripts in a normal
alignment, it will try to align that exon with other pieces and not
introduce a gap in the other sequences to accommodate the exon.

Ideally the results should look like this:


Using the API, is it possible to get this type of aligned transcripts back?

Any other suggestions on how to do this are also welcome!


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