An open source software for recognition of consensus motifs in proteomics
MotiFF is a tool for large scale proteomics that discovers the enriched amino acid patterns containing modified amino acids in the results of proteomic analysis. MotiFF implements calculation of the binomial probabilities and χ2 criterion to identify statistically significant amino acid patterns or motifs for the modified peptides. The algorithm was implemented in Python as an open-source command-line tool available at https://github.com/lineva642/PTM.
Download from Github repository https://github.com/lineva642/PTM. In the directory containing setup.py file run the following command:
pip install .
MotiFF [dataset] [fasta] [-h] [--name_sample NAME_SAMPLE] [--interval_length INTERVAL_LENGTH] [--modification MODIFICATION] [--modification_site MODIFICATION_SITE] [--working_dir WORKING_DIR] [--algorithm ALGORITHM] [--p_value P_VALUE] [--occurrences OCCURRENCES] [-v {0,1,2}]
positional arguments:
dataset Path to experimental dataset
fasta Path to FASTA
optional arguments:
-h, --help show this help message and exit
--name_sample NAME_SAMPLE
Name of examined sample
--interval_length INTERVAL_LENGTH
Number of amino acids before & after modified amino acid (default=6)
--modification MODIFICATION
Name of modification(ex.PHOSPHORYLATION)
--modification_site MODIFICATION_SITE
Modified amino acid (ex.S,T)
--working_dir WORKING_DIR
Working dir for program (default=".")
--algorithm ALGORITHM
Enter algorithm name: binom or chi2(default="chi2")
--p_value P_VALUE Enter p_value(default=0.000005)
--occurrences OCCURRENCES
Enter number of motif occurrences in experimental dataset (default=20)
-v {0,1,2}, --verbosity {0,1,2}
Output verbosity
MotiFF produces summary table (motifs.csv) with discovered amino acid motifs and additional information:
| Column name | Description |
|---|---|
| motif | Enriched amino acid pattern containing modified amino acid |
| p_value | Probability of the identified motif |
| fg_matches | Number of modified peptides containing this enriched amino acid pattern |
| fg_size | Number of modified peptides among which search is carried out |
| bg_size | Number of FASTA peptides among which search is carried out |
| bg_matches | Number of FASTA peptides containing this enriched amino acid pattern |