Tools/Papers for function analysis
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PAPER: Computational methods for protein function analysis. - http://www.ncbi.nlm.nih.gov/pubmed/11166647
PAPERhttp://pir.georgetown.edu/pirwww/about/doc/2004-CBAC-iproclass.pdf
Server:iProClass http://pir.georgetown.edu/iproclass/
Link to servers and explainations:http://www.ebi.ac.uk/Tools/protein.html
SERVER: PIMA - This tool allows you to search our library of functional diagnostic profiles with a protein sequence. A match to one or more of these profiles provides you with an effective multi-alignment of your query sequence to the best-matched profile's defining set of proteins along with its annotations http://bmerc-www.bu.edu/bioinformatics/profile_request.html
SERVER: Predict Protein - http://www.predictprotein.org/