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.bhag...@uni-marburg.de <aditya.bhag...@uni-marburg.de> Sent: Tuesday, May 21, 2024 9:20 AM To: Liu, Haibo <haibo....@umassmed.edu> Cc: Vincent Carey <st...@channing.harvard.edu>; bioc-devel@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-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 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat/ >> .ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=05%7C02%7Chaibo.liu%40 >> umassmed.edu%7C47f0c877418b4558bdac08dc79859dee%7Cee9155fe2da34378a6c4 >> 4405faf57b2e%7C0%7C0%7C638518862010686203%7CUnknown%7CTWFpbGZsb3d8eyJW >> IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C% >> 7C%7C&sdata=zDryByDBnvrbLsS4GN5W4EKzwc5%2FcpTdl3vgNrCEb%2BQ%3D&reserve >> d=0 >> > > -- > The information in this email is intended only for the p...{{dropped:15}} > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Aditya Bhagwat Translational Proteomics ∙ Philipps-University Marburg Biological Pharmacological Center ∙ Room A406 Tel.: +49 6421 28 27403 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
