Skip to content
Prev 11602 / 21312 Next
Original Raw

[Bioc-devel] Creating an org.Hs.uniprot.db package

Rainer Johannes 
Hi Aditya,

you could check the more recent ensembldb EnsDb databases to see if
there is something in them you might need/want.
I've added protein annotations to them (as provided by Ensembl). They
contain the Ensembl protein domains, the AA sequence, all protein domain
families (as defined/linked in Ensembl) and the mapping from Ensembl
protein IDs to Uniprot (which is unfortunately not always 1:1) - and you
get the mapping to the encoding transcripts for free ;)

To play around with it I suggest you get one of the EnsDb databases from
AnnotationHub:

library(AnnotationHub)
query(AnnotationHub(), "EnsDb.Hsapiens")

and fetch one of those. Have also a look at the ensembldb vignette(s)
for starters.

cheers, jo
On 09/13/2017 07:02 AM, Aditya Bhagwat wrote:

Thread (7 messages)

Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 12 Rainer Johannes Creating an org.Hs.uniprot.db package Sep 12 Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 12 Vincent Carey Creating an org.Hs.uniprot.db package Sep 13 Karim Mezhoud Creating an org.Hs.uniprot.db package Sep 13 Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 13 Karim Mezhoud Creating an org.Hs.uniprot.db package Sep 13