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Hotpep specifications

Information


Unique identifier OMICS_17113
Name Hotpep
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A text file with predicted protein sequences (for annotation).
Input format Fasta
Output data One directory for each enzyme class in the CAZy database, a file containing a summary of the results and a file with all the families found for each accession number. Each of the class directories contains files with the hits for each family, a summary and a directory with functional predictions. The folder with functional predictions contains files for each EC number found and a summary.
Operating system Windows
Programming languages Ruby
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Pete Busk

Publication for Hotpep

Hotpep citations

 (6)
library_books

Enzyme Activities at Different Stages of Plant Biomass Decomposition in Three Species of Fungus Growing Termites

2018
Appl Environ Microbiol
PMCID: 5812949
PMID: 29269491
DOI: 10.1128/AEM.01815-17

[…] Homology to Peptide Pattern (Hotpep []) with peptide pattern recognition (PPR) generated peptide patterns for all enzyme families in the Carbohydrate-Active enZymes (CAZy) database () was used to identify CAZymes in the translate […]

library_books

Diversity of microbial carbohydrate active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge

2017
Biotechnol Biofuels
PMCID: 5480151
PMID: 28649277
DOI: 10.1186/s13068-017-0840-y

[…] rther, we were only able to assign a function to 54% of the CAZymes by our unique bioinformatics approach, which demonstrates that there is still much to uncover about the functionality of CAZymes as HotPep only assigns a function to a PPR group if a CAZyme within the group have already been characterized. This suggests that the ADs are a good place to look for novel plant biomass degrading and mo […]

library_books

Aspergillus hancockii sp. nov., a biosynthetically talented fungus endemic to southeastern Australian soils

2017
PLoS One
PMCID: 5381763
PMID: 28379953
DOI: 10.1371/journal.pone.0170254

[…] ptide pattern recognition subfamily grouping correlates to function []. This non-alignment-based sequence analysis method produces lists of peptide patterns that enable another PPR program designated HotPep [] to mine entire genomes efficiently for all types of carbohydrate active enzymes, and can also predict the protein subfamily to which an enzyme belongs. As each protein family covers several […]

library_books

Genome and secretome analyses provide insights into keratin decomposition by novel proteases from the non pathogenic fungus Onygena corvina

2015
Appl Microbiol Biotechnol
PMCID: 4628079
PMID: 26177915
DOI: 10.1007/s00253-015-6805-9

[…] Gene annotation by Hotpep was done as previously described (Busk and Lange ). The predicted protein sequences of the hits were confirmed by BLAST. Full-length genes of the validated proteases were obtained by assembling […]

call_split

Classification of fungal and bacterial lytic polysaccharide monooxygenases

2015
BMC Genomics
PMCID: 4424831
PMID: 25956378
DOI: 10.1186/s12864-015-1601-6
call_split See protocol

[…] Hotpep analysis was performed as previously described []. The procedure can be described by the following steps:Fungal genomes were split into fragments of 2000 bases with 100 bases overlap. The fragm […]

library_books

Several Genes Encoding Enzymes with the Same Activity Are Necessary for Aerobic Fungal Degradation of Cellulose in Nature

2014
PLoS One
PMCID: 4252092
PMID: 25461894
DOI: 10.1371/journal.pone.0114138

[…] The genomes of the 39 fungi were screened with Hotpep for members of the GH families 1–131 and for the AA families 9–11 that include the LPMOs. The N50 for the genomes varied between 6,000 and 10,000 kilobase pairs (kbp) indicating different quali […]

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Hotpep institution(s)
Department of Chemical and Biochemical Engineering, Technical University of Denmark, Soltofts Plads, Lyngby, Denmark
Hotpep funding source(s)
Supported by project number Mar 14319 from Nordic Innovation, SYNFERON – from the Danish Innovation Fund and by The Villum Foundation.

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