software for analysing sequence features...

[Sensational Gravity Boy]

Hi all, 

would anyone know of software for analyze protein sequences and searching 
for things like possible phosphorylation sites, nuclear localization 
signals, etc... I seen lots of papers where people describe their protein 
sequence in detail and I wonder if they've just analyzed visually, or 
through some sort of program...something akin to the programs that will 
analyze the coding potential of a DNA sequence. 

your help is much appreciated,

Ed Taboada
Dept of Biology
University of Ottawa
Ottawa, Canada