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.
|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|
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: