conserved domain in multiple sequences

[tamarbsor]

Hi,

i have a list of about 300 proteins. i would like to know which of them contain specific domains (1 or more domains that i would like to check- specific domains). which tool do i use? and how do i do it?

thanks in advance,
Tamar

[GenoMax]

Start here: http://www.molbiol-tools.ca/Motifs.htm

[maubp]

Further to that, what kind of domains are you talking about? If predefined ones like Pfam domains then there would be a model file and associated tool to use (e.g. Hmmer3).

Discovering new domains is another task, MEME/MAST would be one option to explore if at was what you meant.