[ensembl-dev] (no subject)
Matthew.Healy at bms.com
Mon Apr 2 18:39:49 BST 2012
I am new to BIOMART and the Ensembl Perl API, so probably I am just confused. I would be grateful for some enlightenment from those with more experience.
I am trying to map protein features into chromosomal nucleotide coordinates.
First I use the fetch_by_stable_id() method of the transcript adaptor to get a transcript object given its ENSTxxx identifier.
Then I use the get_all_ProteinFeatures() method of that transcript object to get all its protein features.
Then I use the pep2genomic method of Bio::EnsEMBL::TranscriptMapper to map these coordinates into nucleotide space.
Usually this works as I would expect it to work: if a protein domain feature spans multiple exons, then I get back multiple pairs of genomic coordinates.
When the domain overlaps the start or the end of the translation, I also get a gap object in transcript nucleotide coordinates (start and end both zero or both minus one or both length of transcript plus one), indicating some of that domain is missing from this translation.
However, I have also found an oddity in BioMart. I downloaded a table of transcript coordinates from BIOMART. In most cases,
these coordinates are exactly the same as the coordinates displayed by the genome browser. But I have seen a few cases where
they are different.
For example, in the ENSEMBL genome browser right now the coordinates for ENST00000392973 are given as
Chromosome 16: 90,071,281-90,086,526 reverse strand. But when I downloaded all transcripts for
ENSG00000003249 using http://useast.ensembl.org/biomart/martview/ the relevant row of output is:
Ensembl Gene ID Ensembl Transcript ID Ensembl Protein ID Gene Start (bp) Gene End (bp) Strand Transcript Start (bp) Transcript End (bp) Chromosome Name
ENSG00000003249 ENST00000392973 ENSP00000376699 90071273 90086536 -1 90071281 90076619 16
In which Transcript End (bp) is 90076619 versus 90,086,526 displayed in browser views.
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