how to access protein sequences in batch

Model Organism: Worms Methods & Reagents
1

Hi everyone,
I am trying to analyze a list of proteins (n=500) for their sequence to sort out membrane proteins. I have their gene names as well as wormbase IDs in a list generated from Wormmine. Is there a way to do this in a batch mode so that I don’t have to go into wormbase and pull out the sequence one by one? Any suggestions will be greatly appreciated. Thank you so much! -X

2

Connect to the FTP (go to Downloads then “Public FTP Site” ). You can download the protein.fa.gz for whichever release you want. For example, the path to the current production release would be:
wormbase/releases/WS257/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS257.protein.fa.gz.

Mike

3

Use WormMine. From the Home page:

  1. paste your WormBase IDs in ‘Analyze a List’ field, select ‘Protein’ from pulldown, and click ‘Analyze’
  2. save the list that’s generated
  3. from list report, select ‘Manage Columns > Add a column > +Sequence > Residues > Add 1 new column > Apply changes’
  4. ‘Export’ results
4

Thank you very much, both of you! I’ll try the wormMine as this will give me only the 500 proteins I need to analyze. Thanks again! -Xue