Copyright (C) 2019 University of Southern California

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
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This program is distributed in the hope that it will be useful,
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The PANTHER Hidden Markov Models (including names, descriptions and abstracts) may be copied and redistributed freely in accordance with the Interpro Copyright agreement.  Here is an extract from the InterPro documentation: InterPro - Integrated Resource Of Protein Domains And Functional Sites Copyright (C) 2001 The InterPro Consortium. This manual and the accompanying database may be copied and redistributed freely, without advance permission, provided that this Copyright statement is reproduced with each copy. The InterProScan software is distributed under GNU license as the included scanning tools. Therefore you do not need a special license for commercial use but please cite the resource and keep the Copyright statement.

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PANTHER 14.1
http://www.pantherdb.org
01/18/2019
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PANTHER HMM library Version 14.1
Contains the PANTHER HMMs for 15524 protein family HMMs, divided into 107627 functionally distinct protein subfamily HMMs.

The PANTHER HMMs are in HMMER format.  The PANTHER library is available in 2 formats:
-HMMER HMMS in ASCII/text format (PANTHER14.1_ascii.tgz) 
-library for coding snp analysis (PANTHER14.1_hmmscoring.tgz): HMMER HMMs in ASCII/text format plus multiple-sequence alignment file and tree file 

By downloading the PANTHER HMMs you agree that the use of the same is subject to the terms and conditions of the GNU General Public License Version 2, June 1991 promulgated by the Free Software Foundation.
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The PANTHER Classification System is formatted in a library structure:

PANTHER14.1/books/ - Each protein family is considered a book with their own unique PTHR accession number.  In each protein family book, there will be the following information:

   *hmmer.hmm - a HMMER Hidden Markov Model for a protein family. 

   *cluster.pir - (only in version of library for snp analysis) the multiple sequence alignment for the protein family
  
   *tree.tree - (only in version of library for snp analysis) the tree file for the protein family

   *SF directory - a listing of all the subfamily members in the protein family.

      Within each SF (subfamily) directory, there is the following:

     *hmmer.hmm - a HMMER Hidden Markov Model for a protein subfamily.


PANTHER14.1/globals - besides containing individual protein family information, there is also a globals directory that contains information pertaining to the whole PANTHER classification library. The following files are in the globals directory:

   *names.tab - a list of all the protein family and subfamily names for the PANTHER classification library.  Protein family names are denoted by 'PANTHER accession.mag.mod' followed by the family name. Subfamilies are denoted by 'PANTHER accession.SF#.mod'.  
      Ex. PTHR10003.mag.mod	CU/ZN SUPEROXIDE DISMUTASE
      Ex. PTHR10003.SF38.mod	EXTRACELLULAR SUPEROXIDE DISMUTASE


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To score protein sequences, or analyze coding SNPs against this entire library of PANTHER HMMs, download the PANTHER scoring tools from:
http://www.pantherdb.org/downloads/

The latest version of the PANTHER HMMs can be downloaded from http://www.pantherdb.org/downloads/.  

If you have any questions, please contact us at: feedback@pantherdb.org