Hotpep-carbohydrate Files

Hotpep for annotation of carbohydrate-active enzymes

The application consists of the executable files “hotpep.exe” and the directory "CAZY_PPR_patterns" including subdirectories and files.
The tool was written for Windows and has been tested under Windows 7 and Windows 10.


Installation:
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.exe”, this ”README” file, the directory "CAZY_PPR_patterns" including subdirectories and files
and the test input file ”Fungus fungus.txt” in the new folder and is ready for annotation.


To annotate carbohydrate-active enzymes:
1)  Place a file containing the sequences you want to analyze in the same folder as ”hotpep.exe”.
	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 ”Fungus fungus.txt”.


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

3) Enter the name of the file to screen and run the analysis.

4) Press ”enter” to close the dos window when Hotpep has finished.

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


Please, see Busk et al. (2017) for interpretation of the results.


Expanded families:

Expanded PPR patterns have been made for the following PPR families and are included in the current version of Hotpep:
AA9, AA10 and AA11	- Included 05.May.2017; Busk PK. Lange L. (2015). Classification of fungal and bacterial lytic polysaccharide monooxygenases. BMC Genomics 16, 368.
CE15 			- Included 07.Aug.2017; Agger JW. Busk PK. Pilgaard B. Meyer AS. Lange L. (2017). A new functional classification of glucuronoyl esterases by peptide pattern recognition. Frontiers in Microbiology 8, 309.
GH62 			- Included 07.Aug.2017; Wilkens et al., Unpublished.

If you wish to use the PPR patterns described in Busk et al., 2017, please download CAZY_PPR_patterns_version1.zip, unzip it and install it instead of the directory "CAZY_PPR_patterns". Remember to rename the directory to  "CAZY_PPR_patterns".


Use of Hotpep for annotation of carbohydrate-active enzymes for academic purposes is free as long as you cite:
Busk, P.K., Pilgaard, B., Lezyk, M.J., Meyer, A.S. and Lange, L. (2017). 
Homology to Peptide Pattern for Annotation of Carbohydrate-Active Enzymes and Prediction of Function.
BMC Bioinformatics. DOI: 10.1186/s12859-017-1625-9.



Good luck!


Peter Busk, 05.Apr.2017






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 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.