{"id":18726031,"url":"https://github.com/fomightez/hhsuite3-binder","last_synced_at":"2026-04-11T22:02:15.491Z","repository":{"id":71622395,"uuid":"313706291","full_name":"fomightez/hhsuite3-binder","owner":"fomightez","description":"Repo for running command line-based HH-suite3 software in Jupyter environment provided via Binder.","archived":false,"fork":false,"pushed_at":"2023-11-09T20:33:50.000Z","size":604,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-12-28T13:24:24.198Z","etag":null,"topics":["bioinformatics","bioinformatics-analysis","bioinformatics-scripts","genomics","pandas","pandas-dataframes","protein-sequences","python"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fomightez.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-11-17T18:22:08.000Z","updated_at":"2021-12-03T22:10:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"23ed87cc-784d-4b83-ab5c-c37662275464","html_url":"https://github.com/fomightez/hhsuite3-binder","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fomightez%2Fhhsuite3-binder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fomightez%2Fhhsuite3-binder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fomightez%2Fhhsuite3-binder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fomightez%2Fhhsuite3-binder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fomightez","download_url":"https://codeload.github.com/fomightez/hhsuite3-binder/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239592972,"owners_count":19664855,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bioinformatics-analysis","bioinformatics-scripts","genomics","pandas","pandas-dataframes","protein-sequences","python"],"created_at":"2024-11-07T14:12:55.217Z","updated_at":"2025-11-11T20:30:14.668Z","avatar_url":"https://github.com/fomightez.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hhsuite3-binder\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/hhsuite3-binder/main?filepath=index.ipynb)\n\n*tl;dr:*  \nClick any `launch binder` badge on this page to run command line-based HH-suite3 software inside your browser.\n\n------\n\n***HH-suite3 for fast remote homology detection and deep protein annotation demonstrated in your browser via Jupyter.***\n\nThis 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/).  \nIn 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.  \n\n-------\n\nSoftware\n--------\n\nThe [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).\n\n\nThe HH-suite3 software references are listed in full [here](https://github.com/soedinglab/hh-suite/wiki#user-guide) under 'References'.\n\nUsers of HH-suite3 here should probably cite:\n\n- Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)\nHH-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)\n\n\n***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.***\n\nI, 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.\n\n\nUsage\n-----\n\nThis 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.\n\nIn 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.\n\n**The Binder-launchable version too limiting for your needs?**\n\nThe 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).\n\nWeb-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/). \n\n\nRelated\n-------\n\n- My [hhsuite3-utilities sub-repo](https://github.com/fomightez/sequencework/tree/master/hhsuite3-utilities)\n\n- [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.\n\n\nTechnical Details\n-----------------\n\nThis 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.\n\nI 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).\n\nClick this button below to begin using HH-suite3 (or BLAST, as well):\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/hhsuite3-binder/main?filepath=index.ipynb)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffomightez%2Fhhsuite3-binder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffomightez%2Fhhsuite3-binder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffomightez%2Fhhsuite3-binder/lists"}