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[Bioc-devel] AnnotationHub: uniprot seqs ?

5 messages · @dity@@bh@gw@t m@iii@g oii u@i-m@rburg@de, Vincent Carey, Liu, Haibo

Original
@dity@@bh@gw@t m@iii@g oii u@i-m@rburg@de
# 
Hey guys,

Do we have Uniprot sequences in AnnotationHub ?
Not being able to find them.

Thankyouverymuch : )

Aditya
Vincent Carey
# 
On Tue, May 21, 2024 at 4:18?AM Aditya Bhagwat via Bioc-devel <
bioc-devel at r-project.org> wrote:

            

      
      
      
    

        
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.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Liu, Haibo
    

    

      
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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 at r-project.org> On Behalf Of Vincent Carey
Sent: Tuesday, May 21, 2024 7:02 AM
To: aditya.bhagwat at uni-marburg.de
Cc: bioc-devel at 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 at r-project.org> wrote:

        

            

      
      
      
    

        
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.

            

      
      
      
    

        

      
      
    

        
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The information in this email is intended only for the p...{{dropped:15}}

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      @dity@@bh@gw@t m@iii@g oii u@i-m@rburg@de
    

    

      
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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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      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 at uni-marburg.de <aditya.bhagwat at uni-marburg.de>
Sent: Tuesday, May 21, 2024 9:20 AM
To: Liu, Haibo <Haibo.Liu at umassmed.edu>
Cc: Vincent Carey <stvjc at channing.harvard.edu>; bioc-devel at 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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
--
Aditya Bhagwat
Translational Proteomics ? Philipps-University Marburg
Biological Pharmacological Center ? Room A406
Tel.: +49 6421 28 27403