C. elegans secreted proteins

Model Organism: Worms Scientific Discussion
1

Help!

I need to do a BLASTP search of the “secretome” (i.e. all secreted proteins) of C. elegans. Can anyone let me know whether there is a simple way of doing this?

Many thanks in advance

John

2

WormBase doesn’t provide a way to restrict your blast to subset of proteins.

You can do this (fairly) easily yourself if you have the gumption.

  1. collect the sequences you need

  2. downloaded NCBI blast

  3. built your BLAST database (really just a single command)

  4. BLAST your sequence

The hardest / most time-consuming part will be step 1.

Please let me know if you’d like additional details.

3

OK - This is the bit I’m struggling with. I can cope with a local BLAST search but how do I download all the secreted proteins and none of the others?

4

you could try to use only proteins based on their GO annotation, as example:
basal lamina (GO:0005605) and proteinaceous extracellular matrix (GO:0005578) definitively contain secreted proteins.
But of course that is dependent on the GO annotation.
Or you could use the protein-set and run it through targetp or some similar software to predict potentially secreted proteins.
We also include signalp predictions in the databas (I need to check how to query them best).
Another idea would be searching beta.uniprot.org for:
organism:“Caenorhabditis elegans” AND keyword:secreted

the keyword makes it include GO+SignalP predictions if I understood it correctly

But all of the above methods of course can’t guarantee completeness.

Hope

5

Hi,
I’ve just added a section to the WormBase wiki explaining how to query for all genes with a signalP domain.
See http://www.wormbase.org/wiki/index.php/FAQs#How_do_I_find_all_genes_with_transmembrane_or_signalp_domains.3F

Ant

6

Thanks all!

John