[Bioc-devel] AnnotationHub: uniprot seqs ?

[Liu, Haibo]

If you have many sequences to download, it can be very slow if you use Uniprot.ws to query the database. I used a walk-around method to download the proteome of a species using FTP in my dagLogo package: https://github.com/jianhong/dagLogo/blob/devel/R/prepareProteomeByFTP.R.

Haibo

-----Original Message-----
From: aditya.bhagwat using uni-marburg.de <aditya.bhagwat using uni-marburg.de>
Sent: Tuesday, May 21, 2024 9:20 AM
To: Liu, Haibo <Haibo.Liu using umassmed.edu>
Cc: Vincent Carey <stvjc using channing.harvard.edu>; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

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-bounces using r-project.org> On Behalf Of
> Vincent Carey
> Sent: Tuesday, May 21, 2024 7:02 AM
> To: aditya.bhagwat using uni-marburg.de
> Cc: bioc-devel using 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 using 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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--
Aditya Bhagwat
Translational Proteomics ∙ Philipps-University Marburg
Biological Pharmacological Center ∙ Room A406
Tel.: +49 6421 28 27403