hhsuite3-binder
tl;dr:
Click any launch binder badge on this page to run command line-based HH-suite3 software inside your browser.
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.
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.
Software
The HH-suite3 software will be installed already in each active session launched from this repository. The HH-suite3 software is available directly from the authors here.
The HH-suite3 software references are listed in full here 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
Clarifying Software Attribution: I, Wayne, am not involved in the HH-suite3 software at all. Those in the lab of Johannes Söding 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 and utilized in the notebooks in this repository to process the results and allow easily converting the results to other Python-friendly forms.
Usage
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, 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 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. If you need other installation options, such as configured for a cluster, other installation options are type is discussed here.
Web-based automated searching for remote homologs via HHpred is also available via the MPI Bioinformatics Toolkit.
Related
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Collection of Jupyter notebooks by Gorbalenya-Lab that were used for their LAMPA paper. 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 which describes using HH-suite to annotate multi-domain proteins where the domain boundaries aren't initially known.
Technical Details
This repository is set up to make use of the binder service offered by 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.
Click this button below to begin using HH-suite3 (or BLAST, as well):