Protein Classification.ppt

Protein Classification A comparison of function inference techniques Why do we need automated classification? Sequencing a genome is only the first step. Between 35-50% of the proteins in sequenced genomes have no assigned functionality. Direct observation of function is costly, time consuming, and difficult. Protein Domains Inference through sequence similarity ProtoMap: Automatic Classification of Protein Sequences, a Hierarchy of Protein Families, and Local Maps of the Protein Space (1999) Final Goal Observations Sometimes you don’t know where the domains are. It is generally accepted that two sequences with over 30% identity are likely to have the same fold. Homologous proteins have similar functions. Homology is a transitive relationship. Departures Authors do not attempt to define protein domains or motifs. Not dependant on predefined groups or classifications. Chart the space of all proteins in SWISSPROT, as opposed to individual families Produce global organization of sequences. Algorithm Overview We construct a weighted graph where the nodes are protein sequences and the edges are similarity scores. Cluster the network considering only those edges above some threshold. Decrease similarity threshold and repeat. Measuring Sequence Similarity Expectation value used. This the normalized probability of the similarity occurring at random. Lower value implies logarithmically stronger similarity. Blosum62 Scoring Matrix Finding Homologies Very difficult to distinguish a clear threshold between homology and chance similarity. Authors chose e = .1, .1, and .001 for SW, FASTA, and BLAST, respectively. Spent a lot of time empirically determining these thresholds. Clustering ProtoMap: Results Produces well-defined groups which correlate strongly to protein families in PROSITE and Pfam. Results:Immunoglobin Superfamily ProtoMap: Limitations Analysis performs poorly by families dominated by short/local domains (PH, EGF, ER_TARGET, C2, SH2, SH3, ect…) High scoring,