Case study: Comparison between  thermophilic and mesophilic organisms

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Keywords:

computable sequence properties, visualisations (built in and generic), comparison of numeric distributions

Initial situation:

Complete genomes for mesophilic and thermophilic organism are available and allow one to run large-scale comparisons.

Questions:

• Are proteins of mesophilic and thermophilic proteins longer or shorter or equally long?
• Are thermophilic proteins more hydrophobic than mesophilic proteins?

Data:

We used the proteome sequences of the organisms used by Thompson & Eisenberg (1999) and merged the amino acid sequences to 2 FASTA files.

File	Content
meso_prots.fasta	All proteins of the used mesophilic organisms
thermo_prots.fasta	All proteins of the used thermophilic organisms

Steps

Step 1: Data import

Simply import the 2 protein sets to PROMPT by using the FASTA import feature. Choose “Import -> FASTA -> File” and choose “protein” as sequence type in the following dialog.

Step 2: Analysis & Results

Select both input entries and choose from the menu:

"Analyze -> Generic Annotations -> Compare annotations between 2 sets -> Numeric feature comparison"

Then select in both sets the same numerical features that should be compared (here length and HydrophobicityAvg)

 

Summary:

• As seen in this example PROMPT can be used to analyse either small sets of proteins or perform large scale analyses corresponding to the 20 organisms in this example.
• All analyses can be run either interactively, by scripts, pipelines or the Java API directly.

More:

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