PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
TL;DR: The number of pathways associated with subfamilies in PANTHER, a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles, has dramatically expanded.
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Abstract: PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles Since 2005, there have been three main improvements to PANTHER First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distributed as part of InterProScan Third, we have dramatically expanded the number of pathways associated with subfamilies in PANTHER Pathways provide a detailed, structured representation of protein function in the context of biological reaction networks PANTHER pathways were generated using the emerging Systems Biology Markup Language (SBML) standard using pathway network editing software called CellDesigner The pathway collection currently contains approximately 1500 reactions in 130 pathways, curated by expert biologists with authorship attribution The curation environment is designed to be easy to use, and the number of pathways is growing steadily Because the reaction participants are linked to subfamilies and corresponding HMMs, reactions can be inferred across numerous different organisms The HMMs can be downloaded by FTP, and tools for analyzing data in the context of pathways and function ontologies are available at http://wwwpantherdborg
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PANTHER: a library of protein families and subfamilies indexed by function.
Paul Thomas,Michael J. Campbell,Anish Kejariwal,Huaiyu Mi,Brian Karlak,Robin Daverman,Karen Diemer,Anushya Muruganujan,Apurva Narechania +8 more
TL;DR: The PANTHER/X ontology is used to give a high-level representation of gene function across the human and mouse genomes, and the family HMMs are used to rank missense single nucleotide polymorphisms (SNPs) according to their likelihood of affecting protein function.
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TL;DR: InterProScan is a tool that combines different protein signature recognition methods from the InterPro consortium member databases into one resource and can be analysed for protein as well as DNA sequences.
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