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https://github.com/fomightez/hhsuite3-binder

Repo for running command line-based HH-suite3 software in Jupyter environment provided via Binder.
https://github.com/fomightez/hhsuite3-binder

bioinformatics bioinformatics-analysis bioinformatics-scripts genomics pandas pandas-dataframes protein-sequences python

Last synced: 4 months ago
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Repo for running command line-based HH-suite3 software in Jupyter environment provided via Binder.

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README 

        
# hhsuite3-binder



[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/hhsuite3-binder/main?filepath=index.ipynb)



*tl;dr:*  

Click any `launch binder` badge on this page to run command line-based HH-suite3 software inside your browser.



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***HH-suite3 for fast remote homology detection and deep protein annotation demonstrated in your browser via Jupyter.***



This repository is for running HH-suite3 programs, such as hhblits and hhsearch, or analyzing the output of HH-suite3 programs in Jupyter environment provided by [MyBinder.org](https://mybinder.org/).  

In regards to analyzing the output of HH-suite3 programs, having HH-suite3 working inside the Jupyter environment with interactive Python adds some convenient features that are illustrated. A utility script for moving command line-based HH-suite3 results files into Python is also demonstrated, along several ways it can be used to mine additional information from the the output of HH-suite3 programs using Python/Jupyter.  



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Software

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The [HH-suite3](https://github.com/soedinglab/hh-suite/wiki) software will be installed already in each active session launched from this repository. The HH-suite3 software is available directly from the authors [here](https://github.com/soedinglab/hh-suite).



The HH-suite3 software references are listed in full [here](https://github.com/soedinglab/hh-suite/wiki#user-guide) under 'References'.



Users of HH-suite3 here should probably cite:



- Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)

HH-suite3 for fast remote homology detection and deep protein annotation, *BMC Bioinformatics*, 473. [doi: 10.1186/s12859-019-3019-7](https://doi.org/10.1186/s12859-019-3019-7)



***Clarifying Software Attribution: I, Wayne, am not involved in the HH-suite3 software at all. Those in [the lab of Johannes Söding](https://www.mpibpc.mpg.de/soeding) are the developers and source of HH-suite3. See their materials. I simply set up this repository to make the software useable on the command line without installation headaches and in a full-featured, browser-based computational environment.***



I, Wayne Decatur, did  Jupyter/Python-based utilities for use with the results from command line HH-suite3 results files; these available [here](https://github.com/fomightez/sequencework/tree/master/hhsuite3-utilities) and utilized in the notebooks in this repository to process the results and allow easily converting the results to other Python-friendly forms.



Usage

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This repository is set up to allow running the command line version of HH-suite3 software after pressing the `launch binder` button above or below. The target use case is when you want to learn about using HH-suite3, especially `hhblits`. Importantly, the resources needed for `hhblits` to make a good HHM for a sequence goes beyond what MyBinder provides. You'll need to find more computer resources and power to build on what you learn here. Instead of using a good representative of sequence space provided by the latest release of [the Uniclust30 database](https://uniclust.mmseqs.com/), we'll either use a smaller database as an example or bring in pre-made MSAs or HHMs. The Uniclust30 database (currently the `2020_06` version) is generously provided by the software authors via a webserver [here](https://toolkit.tuebingen.mpg.de/tools/hhblits) for making rich MSAs for a sequence.



In the notebooks that can be launched, I have added some examples illustrating how to use the program and process the results easily with Python and convert to other forms. **Additionally, useful resources for using command line HH-suite3 are in those notebooks or analyzing the output from the HH-suite3 programs are presented.** Alternatively, the notebook with most of resources can be viewed statically [here?????](?????). The ['Credits/Resources'????? section right at the top](?????) is a good place to start.



**The Binder-launchable version too limiting for your needs?**



The authors have made the software installable via conda, see [here](https://anaconda.org/bioconda/hhsuite).  If you need other installation options, such as configured for a cluster, other installation options are type is discussed [here](https://github.com/soedinglab/hh-suite/wiki#installation-of-the-hhsuite-and-its-databases).



Web-based automated searching for remote homologs via [HHpred](https://toolkit.tuebingen.mpg.de/tools/hhpred) is also available via [the MPI Bioinformatics Toolkit](https://toolkit.tuebingen.mpg.de/). 



Related

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- My [hhsuite3-utilities sub-repo](https://github.com/fomightez/sequencework/tree/master/hhsuite3-utilities)



- [Collection of Jupyter notebooks by Gorbalenya-Lab that were used for their LAMPA paper](https://github.com/Gorbalenya-Lab/hh-suite-notebooks/). LAMPA paper: [LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins.Gulyaeva AA, Sigorskih AI, Ocheredko ES, Samborskiy DV, Gorbalenya AE. Bioinformatics. 2020 May 1;36(9):2731-2739. doi: 10.1093/bioinformatics/btaa065. PMID: 32003788](https://pubmed.ncbi.nlm.nih.gov/32003788/) which describes using HH-suite to annotate multi-domain proteins where the domain boundaries aren't initially known.



Technical Details

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This repository is set up to make use of the binder service offered by [MyBinder.org](https://mybinder.org/). See their site for more information about Binder.



I borrrowed the 'warning' highlight/introductory text about notebooks at the top of the included notebook from Tim Sherratt's notebook [here](https://github.com/GLAM-Workbench/te-papa-api/blob/main/Exploring-the-Te-Papa-collection-API.ipynb).



Click this button below to begin using HH-suite3 (or BLAST, as well):



[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/hhsuite3-binder/main?filepath=index.ipynb)