1. EMBOSS
1.1. Physico-chemical properties analysis
1.1.1. Use the JEMBOSS tool PEPSTATS and PEPINFO (in PROTEINS category) to predict the physico-chemical properties of c10orf105, with the default parameters. Note down your observations.
1.1.2. Draw a hydropathy plot using PROTEIN-PROPERTIES-PEPWINDOW. Note down your observations.
1.2. Functional Sites analysis
1.2.1. Run the SIGCLEAVE program to identify presence of signal peptide cleavage sites
1.2.2. Run the TMAP program to predict and plot the potential transmembrane segments
1.2.3. Run PROTEIN-MUTATION-SHUFFLESEQ, to generate a random sequence that we could use to compare our c10orf105 sequence analysis
1.2.4. Run TMAP on the shuffled sequence
1.3. Motifs analysis
1.3.1. Run PROTEIN-MOTIFS-patmatmotifs to predict prosite motifs in our unknown sequence. What is the motif that you see ? Do you see any motif in the random sequence ?
1.3.2. Run the PROTEIN-MOTIFS-antigenic to predict any potential antigenic site in our protein. Also, run the random sequence.
1.4. Domains analysis
1.4.1. Search for any helix-turn-helix domains in both the sequences, using PROTEIN-DOMAINS-helixturnhelix.
1.5. Digestion
1.5.1. Generate the peptide cleavage site map for the two sequence using PROTEIN-COMPOSITION-pepdigest.
1.5.2. Perform a restriction enzyme digestion for the mRNA sequence using the NUCLEIC-RESTRICTION-restrict program.
1.6. Secondary Structure analysis
1.6.1. Predict secondary structure of both the proteins using the PROTEIN-2DSTRUCTURE-garnier
1.7. CpG Islands
1.7.1. Use the program CPGPLOT to predict and plot any CpG islands in our mRNA sequence. Try DOTPLOT and ALIGNMENT programs.
1.8. Primer design
1.8.1. Run EPRIMER32, with target sequence set from 500-700.
1.8.2. Start the Unipro UGENE program, from Applications - Education menu option.
1.8.3. Start a “New Project” and then “Open” our c10orf105 mRNA sequence. Select a region, by clicking and dragging the mouse around 2.4 to 2.6k. Right click the region and choose, Analyze - Primer3. Pick the primers.
