


Tutorial



./mp3 <infile> <dataset> <minimum length of protein sequences> <threshold>
infile: Input file containing protein sequences in FASTA format.
dataset: Specify 1 or 2. "1" referes to genomic proteins and "2" refers to metagenomic proteins.
minimum length of protein sequences: Please specify the estimated minimum length of protein sequences in the input file.
threshold: Please specify the threshold at which the results will be classified as pathogenic or non-pathogenic.
>r1|info1|info2 SQKLILDKLSFSVPKNSITSILAPNGSGKTTLLKCLLGLLKPLEETEIKACNKDILPLKPYEKAKLIThe ‘info’ in the above example is any information which the user wishes to specify in the annotation line. If the sequences are not in FASTA format or contain any character other than usual amino acid letter codes, the file will not be accepted and an error message will appear.
NOTE : THE UPLOADED FILE NAME SHOULDN'T HAVE ANY BLANK SPACES (for e.g. "sample file" is not allowed)
Descriptions of the output files.
1. *.HMM.result: This file provides the list of all proteins which are classified as Pathogenic or Nonpathogenic by HMM module.2. *.HMM.summary: This file provides the summary of the HMM module results.
3. *.Hybrid.result: This file provides the list of all proteins which are classified as Pathogenic or Nonpathogenic by the Hybrid module. It also provides the prediction value of SVM, type of domain present in the protein and the final assignment by Hybrid module.
4. *.Hybrid.summary: This file provides the summary of the Hybrid module results.
5. *.SVM.result: This file provides the list of all proteins which are classified as Pathogenic or Nonpathogenic by SVM module along with the SVM prediction value.
6. *.SVM.summary: This file provides the summary of the SVM module results.