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  1. PANTHER (View Publication)
    Full Name of the Resource : Protein sequence evolution mapped to functions and pathways
    Resource Category : Databases -> Protein Sequence Databases -> Protein Domain Databases (Protein Classification)

    Brief Description : PANTHER (Protein ANalysis THrough Evolutionary Relationships) relates protein sequence evolution to function evolution. Evolutionary relationships between sequences are represented by protein family trees, and these trees are annotated by expert biologists to reflect the divergence of function. Specific protein subfamilies are annotated with molecular function and biological process ontology terms, and are mapped to pathways. Trees (including multiple sequence alignments and biologist annotation) and detailed pathways can be viewed interactively on the web, or downloaded as data. We have also implemented web services for (1) protein sequence classification using subfamily Hidden Markov Models (HMMs), (2) analysis of mRNA or protein expression data using ontology and pathway classifications and pathway diagrams, and (3) scoring of nonsynonymous coding SNPs for likely functional effects using the HMMs and multiple sequence alignments.
    Subject Area : Protein Sequence Evolution


    Institute/s :
    SRI International, Menlo Park, USA
    Address of Institute/s :
    SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3453, USA
    Country : United States

    Associated Institutes :

    • Evolutionary Systems Biology Group, SRI International, USA
    • dictyBase, Northwestern University
    • Berkeley Bioinformatics and Open-source Projects (BBOP), Lawrence Berkeley National Laboratory, USA

    Associated Country : USA


    Authors/Contributors : Paul D. Thomas
    Contact Email : paul.thomas@sri.com
    Year : 2010
    Language : English

    Keywords : Algorithms; Amino Acid Sequence; Animals; Computational Biology / methods / statistics & numerical data; Database Management Systems; Databases, Protein; Genetic Variation; Humans; Markov Chains; Mice; Mutation, Missense / genetics; Peptide Library; Polymorphism, Single Nucleotide / genetics; Predictive Value of Tests; Proteins / classification / genetics / physiology; Sequence Alignment; Software; Terminology as Topic