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Sequence analysis and function prediction using EMBOSS

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.

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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

 

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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

 

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1.2.4. Run TMAP on the shuffled sequence

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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 ?

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1.3.2. Run the PROTEIN-MOTIFS-antigenic to predict any potential antigenic site in our protein. Also, run the random sequence.

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1.4. Domains analysis

1.4.1. Search for any helix-turn-helix domains in both the sequences, using PROTEIN-DOMAINS-helixturnhelix.

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1.5. Digestion

1.5.1. Generate the peptide cleavage site map for the two sequence using PROTEIN-COMPOSITION-pepdigest.

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1.5.2. Perform a restriction enzyme digestion for the mRNA sequence using the NUCLEIC-RESTRICTION-restrict program.

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1.6. Secondary Structure analysis

1.6.1. Predict secondary structure of both the proteins using the PROTEIN-2DSTRUCTURE-garnier

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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.

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1.8. Primer design

1.8.1. Run EPRIMER32, with target sequence set from 500-700.

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1.8.2. Start the Unipro UGENE program, from Applications - Education menu option.

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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.

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