{"id":21861124,"url":"https://github.com/sib-swiss/pftools3","last_synced_at":"2025-04-14T19:22:12.220Z","repository":{"id":46266009,"uuid":"196569750","full_name":"sib-swiss/pftools3","owner":"sib-swiss","description":"A  suite of tools to build and search generalized profiles","archived":false,"fork":false,"pushed_at":"2023-06-07T09:34:56.000Z","size":42820,"stargazers_count":10,"open_issues_count":9,"forks_count":7,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-28T07:41:38.912Z","etag":null,"topics":["motif","profile","protein-domains","sequence-analysis"],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sib-swiss.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog","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":"2019-07-12T11:43:02.000Z","updated_at":"2024-09-18T05:57:25.000Z","dependencies_parsed_at":"2023-10-21T01:49:39.879Z","dependency_job_id":null,"html_url":"https://github.com/sib-swiss/pftools3","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sib-swiss%2Fpftools3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sib-swiss%2Fpftools3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sib-swiss%2Fpftools3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sib-swiss%2Fpftools3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sib-swiss","download_url":"https://codeload.github.com/sib-swiss/pftools3/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248943415,"owners_count":21186958,"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":["motif","profile","protein-domains","sequence-analysis"],"created_at":"2024-11-28T03:09:59.551Z","updated_at":"2025-04-14T19:22:12.197Z","avatar_url":"https://github.com/sib-swiss.png","language":"C","readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pftools/README.html)\n[![install with EasyBuild](https://img.shields.io/badge/install%20with-EasyBuild-brightgreen.svg?style=flat)](#easybuild)\n[![install with Docker](https://img.shields.io/badge/install%20with-Docker-brightgreen.svg?style=flat)](#using-docker)\n[![install with Singularity](https://img.shields.io/badge/install%20with-Singularity-brightgreen.svg?style=flat)](#using-singularity)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/pftools/badges/license.svg)](https://anaconda.org/bioconda/pftools)\n[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/pftools.svg?style=flat)](https://anaconda.org/bioconda/pftools)\n\nPfTools\n=========================================\n\n## Table of Contents\n\n   * [Foreword](#foreword)\n   * [Installation](#installation)\n     * [Using Docker](#using-docker)\n     * [Using Singularity](#using-singularity)\n     * [Bioconda](#bioconda)\n     * [EasyBuild](#easybuild)\n     * [Manually](#manually) \n   * [Generalized profile syntax](#generalized-profile-syntax)\n   * [Algorithms description](#algorithms-description)\n   * [Applications of the Pftools](#applications-of-the-pftools)\n   * [Authors](#authors)\n\n# Foreword\n\n(C) Copyright SIB Swiss Institute of Bioinformatics\navailable from  https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.\n\n\nVersion 3 contains the original FORTRAN 77 pftools (release 2.3)\nand the new pftoolsV3 programs.\n\n# Installation\n\n### Using Docker\n\nFirst you must have [Docker](https://docs.docker.com/get-docker/) installed and running.  \nSecondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).  \nThen:\n```sh\n# get the chosen pftools container version\ndocker pull quay.io/biocontainers/pftools:3.2.11--pl5321r41h4b1256a_2\n#   or\ndocker pull sibswiss/pftools:3.2.12\n# use an pftools's tool e.g. pfscan \ndocker run quay.io/biocontainers/pftools:3.2.11--pl5321r41h4b1256a_2 pfscan -h\n#   or\ndocker run sibswiss/pftools:3.2.12 pfscan -h\n```\n\n### Using Singularity\n\nFirst you must have [Singularity](https://sylabs.io/guides/master/user-guide/quick_start.html) installed and running.\nSecondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).  \nThen:\n```sh\n# get the chosen pftools container version\nsingularity pull docker://quay.io/biocontainers/quay.io/biocontainers/pftools:3.2.11--pl5321r41h4b1256a_2\n#   or\nsingularity pull docker://sibswiss/pftools:3.2.12\n# run the container\nsingularity run pftools_3.2.11--pl5321r41h4b1256a_2.sif\n```\n\nYou are now in the container. You can use an pftools's tool e.g. pfscan doing \n```sh\npfscan -h\n```\n\n## Bioconda\n\n```sh\nconda install -c bioconda pftools\n```\n\n## EasyBuild\n\n```sh\neb --robot --rpath pftoolsV3-3.2.11-foss-2021a.eb\n```\n\n## Manually\n\nSee [here](./INSTALL) for more information\n\n\nAfter installation, in the share/examples/ subdirectory, the *test_V3.sh* shell script is a good starting point for using pfsearchV3/pfscanV3.\n\n# Generalized profile syntax\n\nA description of the generalized profile syntax is given in file:\n\n- [doc/profile.txt](https://raw.githubusercontent.com/sib-swiss/pftools3/master/doc/profile.txt)  (original document)\n- [doc/profile.pdf](https://raw.githubusercontent.com/sib-swiss/pftools3/master/doc/profile.pdf)  (revised and completed version)\n\nit was originally published in\n\n* Bucher P, Bairoch A.\n  A generalized profile syntax for biomolecular sequence motifs\n  and its function in automatic sequence interpretation.\n  Proc Int Conf Intell Syst Mol Biol. 1994;2:53-61.\n  PubMed PMID: [7584418](https://www.ncbi.nlm.nih.gov/pubmed/7584418).\n\n\n# Algorithms description\n\nTechnical details about how profiles can be constructed and parametrized\nare summarized in file:\n\n- [doc/profile.pdf](https://raw.githubusercontent.com/sib-swiss/pftools3/master/doc/profile.pdf)\n\nThe very first paper describing the PFTOOLS algorithms is\n\n* Lüthy R, Xenarios I, Bucher P.\n  Improving the sensitivity of the sequence profile method.\n  Protein Sci. 1994 Jan;3(1):139-46.\n  PubMed PMID: [7511453](https://www.ncbi.nlm.nih.gov/pubmed/7511453); PubMed Central PMCID: PMC2142471.\n\nThe generalized profile alignment method is closely related to other \"classical\"\nalgorithm for aligning sequences. For example, it encompasses the Smith-Waterman\nalgorithm and the Viterbi decoding of profile-HMM (as implemented in HMMER2 for\nexample). Relationships between these algorithm were investigated in\n\n* Bucher P, Hofmann K.\n  A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system.\n  Proc Int Conf Intell Syst Mol Biol. 1996;4:44-51. Review.\n  PubMed PMID: [8877503](https://www.ncbi.nlm.nih.gov/pubmed/8877503).\n\n* Bucher P, Karplus K, Moeri N, Hofmann K.\n  A flexible motif search technique based on generalized profiles.\n  Comput Chem. 1996 Mar;20(1):3-23.\n  PubMed PMID: [8867839](https://www.ncbi.nlm.nih.gov/pubmed/8867839).\n\nRelatively detailed explanations about the profile normalized scores, as well as its\ncomparisons with other popular statistics for sequence alignments can be found in\n\n* Pagni M, Jongeneel CV.\n  Making sense of score statistics for sequence alignments.\n  Brief Bioinform. 2001 Mar;2(1):51-67.\n  PubMed PMID: [11465063](https://www.ncbi.nlm.nih.gov/pubmed/11465053).\n\nThe heuristic score is succinctly described in\n\n* Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L.\n  pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.\n  Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129.\n  PubMed PMID: [23505298](https://www.ncbi.nlm.nih.gov/pubmed/23505298); PubMed Central PMCID: PMC3634184.\n\n# Applications of the Pftools\n\nTwo databases were created based on the PFTOOLS technology: PROSITE and HAMAP\nand they are still actively maintained\n\n1. https://prosite.expasy.org/\n1. https://hamap.expasy.org/\n\nThe PFTOOLS were initially designed with handling capabilities of DNA sequences.\nThe latest released pfsearchV3 feature support for FASTQ and SAM formats. DNA\napplications are for example given in\n\n* Pagni M, Niculita-Hirzel H, Pellissier L, Dubuis A, Xenarios I, Guisan A, Sanders IR, Goudet J, Guex N.\n  Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1.\n  Bioinformatics. 2013 May 15;29(10):1268-74. doi: 10.1093/bioinformatics/btt149.\n  PubMed PMID: [23539304](https://www.ncbi.nlm.nih.gov/pubmed/23539304) ; PubMed Central PMCID: PMC3654712.\n\n* Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM.\n  Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii.\n  MBio. 2017 Nov 7;8(6). pii: e01470-17. doi: 10.1128/mBio.01470-17.\n  PubMed PMID: [29114024](https://www.ncbi.nlm.nih.gov/pubmed/29114024); PubMed Central PMCID: PMC5676039.\n\n# Authors\n\nMas:\n- Philipp Bucher developped the Fortran code\n- Thierry Schuepbach developped the C code\n\nOther contributors:\n- Kay Hofmann\n- Volker Flegel\n- Edouard de Castro\n- Lorenzo Cerruti\n- Marco Pagni\n- Sébastien Moretti\n- Jerven Tjalling Bolleman\n\n[SIB Swiss Institute of Bioinformatics](https://www.sib.swiss/)\n[Vital-IT Group](https://www.vital-it.ch/)\nQuartier Sorge - Batiment Amphipole\n1015 Lausanne\nSwitzerland\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsib-swiss%2Fpftools3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsib-swiss%2Fpftools3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsib-swiss%2Fpftools3/lists"}