Protein function prediction

The goal of this exercise is to use web based tools for protein sequence analysis Take this TrEMBL sequence (Q9X252) and try a BLAST against SwissProt with the complete protein or with the first 70 residues or with the coils filter. Explain the difference. Use TMPred, SignalP, and COILS to help you (or EMBOSS tools). Try to predict post-translational modifications (PTMs) or antigenic peptides Pass this sequence through PFSCAN or InterProScan and search all databases. Use the different profile, motifs, pattern databases to get more information about the domain(s) you found. How do you evaluate the PRINTS tropomyosin annotation in this TrEMBL entry (Q9WZH0)?

List of useful links: basic BLAST or advanced BLAST or PSI-BLAST TMPred prediction tool for transmembrane regions (or TMHMM) COILS prediction tool for coiled-coil regions SignalP prediction tool for signal-peptide cleavage site EMBOSS tools (sigcleave, tmap, pepcoil, antigenic...) BIMAS, SYFPEITHI, MHCBN tools to predict antigenicity CSB tools for PTM prediction Profile, domain, motifs databases and search sites: PFSCAN InterProScan (Pfam, PRINTS, PROSITE, SMART) HITS