Hi all,
I am working on some un-annotated protein sequences. I want to know what kind of tools and programs do one should use. I am using tools like blast, interproscan, CDD search, geno-3D, protfun, etc. Is there any workflow available for annotating proteins.

try ht-go-fat from the usda-ars. It uses blast to provide mappings to go, ec, and kegg terms.

http://genome4.ars.usda.gov/farm/

Hi,

There are numerous annotation pipelines you might try. These are designed to start with DNA, but could probably be used on proteins by stepping farther down there workflow
http://genomes.rockefeller.edu/research.shtml


If you are keen develop your own custom annotation pipeline using tools like the ones you mentioned (interproscan etc.), you might consider learning to use a distributed wokflow builder like Taverna
http://taverna.sourceforge.net/

Come on over to the new bioinformatics forum and we will try to sort you out :)
http://www.scientistsolutions.com/c417-Bioinformatics.html