Case study: Comparison between thermophilic and mesophilic organisms
computable sequence properties, visualisations (built in and generic), comparison of numeric distributions
Complete genomes for mesophilic and thermophilic organism are available and allow one to run large-scale comparisons.
- Are proteins of mesophilic and thermophilic proteins longer or shorter or equally long?
- Are thermophilic proteins more hydrophobic than mesophilic proteins?
We used the proteome sequences of the organisms used by Thompson & Eisenberg (1999) and merged the amino acid sequences to 2 FASTA files.
|meso_prots.fasta||All proteins of the used mesophilic organisms|
|thermo_prots.fasta||All proteins of the used thermophilic organisms|
Step 1: Data importSimply 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)
- 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.
Previous case study:
|Back to the
Case studies Overview
|Next case study:
Fast-Mapping against a large remote database like UniProt-Trembl