Thank you Haibo and Vincent : )
Yes, UniProt.ws is certainly there and did serve me well earlier.
There are times when an offline solution is needed, when operations
are done on larger sets.
Followed my habit to check first whether a relevant AnnotationHub
record exists.
Given the absence of that, I downloaded the relevant fastafile
manually from UniProt.
Read it in with Biostrings and then took it from there.
Which is quite hassle-free, so yes, I can see that there is no need
and not much value to pull it into AnnotationHub.
Thankyou for sharing your experience : )
Cheers,
Aditya
We use Uniprot.ws to access the Uniprot data on demand:
https://bioconductor.org/packages/release/bioc/html/UniProt.ws.html.
Haibo
-----Original Message-----
From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of
Vincent Carey
Sent: Tuesday, May 21, 2024 7:02 AM
To: aditya.bhag...@uni-marburg.de
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] AnnotationHub: uniprot seqs ?
On Tue, May 21, 2024 at 4:18 AM Aditya Bhagwat via Bioc-devel <
bioc-devel@r-project.org> wrote:
Hey guys,
Do we have Uniprot sequences in AnnotationHub ?
That does not seem practical.
Please see
https://bioconductor.org/packages/release/bioc/vignettes/UniProt.ws/inst/doc/UniProt.ws.html
Let us know if that does not meet your need.
Not being able to find them.
Thankyouverymuch : )
Aditya
--
Aditya Bhagwat
Translational Proteomics ∙ Philipps-University Marburg
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