How to use the Web Server
The web server provides all of the options available in the stand-alone version. The instructions for using the web server are provided below.
Application Page
This page is designed to allow to users to submit the protein sequences in FASTA format. These sequences will be analyzed by the HyPe pipeline, predicted peptidoglycan hydrolases will classify in to different classes bases on their site of action. Users can submit either the protein sequences from a completed genome where it is assumed that the protein sequences are complete. OR the user can submit the predicted ORFs (nucleotide) file from assembled metagenomic sequences generated using MetaGeneMark. The various parameters which can be specified are highlighted in the following figure.
Sample file: The sample file can be uploaded using the 'Upload Sample File' option.
Results Page Link
After successful upload of the file on the server, a link to retreive the results will appear as shown below. In case of a large sized input which might take a while to process, users can save the link and access their results later.
Results Page
The results will provide the summary of the analysis and links to download the result files as shown below.
How to install:
The installation instructions are provided on the Download page.
Command line usage for running HyPe
./hype <infile> <dataset>

infile: Input file containing protein or nucleotide sequences in FASTA format.

dataset: Specify 1 or 2. "1" referes to genomic proteins or metagenomic orfs (amino acid file, Length >= 100 amino acids) and "2" refers to metagenomic orfs nucleotide sequence file.

Input file format The sequences should be in fasta file format.
The ‘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 and nucleotide 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. *.Amidase.result: This file provides the output of predictions by HyPe in tabular format.

2. *.nonAmidase.result: This file provides the output of prediction by Random Forest model alone.