https://github.com/ctskennerton/kegg_hmm_models

Create HMMs from KEGG orthologs
https://github.com/ctskennerton/kegg_hmm_models

bioinformatics hidden-markov-model hmm hmmer kegg kegg-ortholog kegg-pathway-database

Last synced: 7 days ago
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Create HMMs from KEGG orthologs

• Host: GitHub
• URL: https://github.com/ctskennerton/kegg_hmm_models
• Owner: ctSkennerton
• License: mit
• Created: 2018-07-07T08:36:55.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-07-07T08:56:12.000Z (over 6 years ago)
• Last Synced: 2024-10-28T11:37:43.765Z (about 2 months ago)
• Topics: bioinformatics, hidden-markov-model, hmm, hmmer, kegg, kegg-ortholog, kegg-pathway-database
• Language: Makefile
• Size: 5.86 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Building HMMs from KEGG data

Using the KEGG REST API it's possible to download genes corresponding

to KEGG orthologs, align them and build HMMs from the alignment. This

process is implemented as a Makefile that allows for efficient and

parallel processing. It is also possible to bulk download and build all

of the HMMs for specific KEGG modules.

#### Dependencies

* [muscle](https://www.drive5.com/muscle/)

* [hmmer](http://hmmer.org)

* [cd-hit](https://github.com/weizhongli/cdhit/releases)

* [python3](https://www.python.org/) (probably already installed on your system)

* [python-requests](http://docs.python-requests.org/en/master/): A library for python that will need to be installed

* [perl](http://www.perl.org/) (probably already installed on your system)

#### Create a HMM for a KEGG ortholog

```

make K00399.kegg_muscle_aligned.hmm

```

#### Create a HMM database for a KEGG module

```

make kegg_modules/M00001/models.hmm.h3p

```

#### Get a list of all KEGG mdules

```

make module_listing.tsv

```