Case Studies

Here we provide a collection of short case-studies that demonstrate the effectiveness of PROMPT and the resulted time saving using PROMPT's broad capability profile. All tutorials are real-world examples from our daily research. The examples start with a short starting situation, propose open question(s) and provide extensive step-by-step instructions required to repeat each analysis. For the reader's convenience, all data files are provided as downloads. The examples build on each other . It is therefore recommended to go through the cases sequentially.
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Comparison Case studies:	Comparison focus:	Script	Play movie
Comparison of isoelectric point distributions	Numeric comparison
Hydrophobicity vs. protein length	Numeric correlation
Protein abundance analysis in yeast	External data
Fold enrichment in GroEL substrates	Categorical comparison
Thermophilic vs. mesophilic organism	Large-scale comparison

Mapping Case studies:	Mapping focus:	Script	Play movie
Fast-Mapping against a large remote database like UniProt-Trembl Potentially up to 50 times faster than BLAST against large databases. __ [Performance evaluation]	SEQs versus REMOTE DB using PROMPT-FM
Map two sequence sets using BLAST or FASTA34	SEQs versus SEQs using BLAST or FASTA34
Map a list of GenBank identifiers with a list of Swiss-Prot accessions	IDs versus IDs using BLAST or FASTA34

Abbreviations: SEQs sequences, IDs identifiers, PROMPT-FM Prompt's Fast-Mapping algorithm.

Advanced Case studies:

Manual testing for statistical significance

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