Hotpep-protease for annotation of proteases and protease inhibitors

Hotpep for annotation of proteases and protease inhibitors

The application consists of the files "hotpep_protease.rb", "annotate.rb" and the directory "protease_patterns" including subdirectories and files.
Use of "Hotpep_protease.rb" requires installation of Ruby 2.5.0 or later and has been tested under Windows 7 and Windows 10. The Ruby installer can be found here: https://rubyinstaller.org/
"Hotpep_protease.exe" does not require installation of Ruby and has been tested under Windows 7 and Windows 10.

Installation of Ruby application:
1) Download ”hotpep” to a folder on your computer.
2) Unzip ”hotpep” and install the content in one folder.
If the installation was successful you will now have "hotpep_protease.rb", "annotate.rb", "hotpep_protease.exe", this ”README” file, the directory "protease_patterns" including subdirectories and files
and the test input file ”test_sequences.txt” in the new folder.
Hotpep-protease is ready to search for proteases and protease inhibitors.

Installation of .exe file:
1) Download ”hotpep_exe” to a folder on your computer.
2) Unzip ”hotpep_exe” and install the content in one folder.
If the installation was successful you will now have "hotpep_protease.exe", this ”README” file, the directory "protease_patterns" including subdirectories and files
and the test input file ”test_sequences.txt” in the new folder.
Hotpep-protease is ready to search for proteases and protease inhibitors.

To annotate proteases and protease inhibitors:
1)  Place a file containing the sequences you want to analyze in the same folder as hotpep_protease.
    The sequences should be in fasta format:
        >name of sequence
        sequence

    The file should be a ”.txt” file or a ".faa" file.
    Please see the examples in the test file ”test_sequences.txt”.

2) When the input is ready annotation is started by double clicking the ”hotpep_protease” icon.
    This will open a small DOS window.

3) Enter the name of the file to screen and press enter.

4) A number of search options will be listed in the DOS window. Please, select the desired option and press enter to run the analysis.

5) Press ”enter” to close the dos window when hotpep_protease has finished.

6) The result are stored in a directory with the same name as the input file.

Interpretation of the results:
Hotpep screens the input sequences for members of all Merops families in the selected "fam_list"-text file in the folder "protease_patterns" or for the specified families.
The results for each family is a text file (path: "/input_name/proteases/[family_name].txt") prepared for import into MS Excel, LibreOffice or similar spreadsheet applications.
The columns in the spread sheet designates the group where the sequence is annotated, the name of the sequence, the sum of the frequencies of the conserved peptides, 
the number of conserved peptides, the protein sequence, length of the sequence and the sequences of the conserved peptides.
In addition, a file with the summary of the results for all families is provided (path: "/input_name/proteases/summary.txt").

Use of hotpep_protease for academic purposes is free as long as you cite:
Busk PK, Lange M, Pilgaard B, Lange L. (2014).
Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature.
PLoS One. 2014 Dec 2;9(12):e114138. doi: 10.1371/journal.pone.0114138.
Or newer publications specifically describing this software.

Good luck!

Peter Busk, 03.December.2019

The software is provided ‘as is’, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. 
In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with 
the software or the use or other dealings in the software.

Copyright 2015, 2016, 2017, 2018,  2019 Peter Kamp Busk
Commercial rights reserved.

Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0),(the "License");
you may not use this file, “hotpep.exe” or the directory "CAZY_PPR_patterns" including subdirectories and files except in compliance with the License.
You may obtain a copy of the License at https://creativecommons.org/licenses/

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.

Due to DTU policies this license is not valid for persons employed by, studying at or otherwise associated to the Technical University of Denmark (DTU). If you are employed by, studying at or otherwise associated to the Technical University of Denmark please, contact the copyright holder to obtain a personal license.