Introduction

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

Publications

  1. SIFTER search: a web server for accurate phylogeny-based protein function prediction.
    Cite this
    Sahraeian SM, Luo KR, Brenner SE, 2015-07-01 - Nucleic acids research
  2. Genome-scale phylogenetic function annotation of large and diverse protein families.
    Cite this
    Engelhardt BE, Jordan MI, Srouji JR, Brenner SE, 2011-11-01 - Genome research

Credits

  1. Sayed M Sahraeian
    Developer

    Department of Plant and Microbial Biology, University of California, United States of America

  2. Kevin R Luo
    Developer

    Department of Molecular and Cell Biology, University of California, United States of America

  3. Steven E Brenner
    Investigator

    Department of Plant and Microbial Biology, University of California, United States of America

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Summary
AccessionBT000237
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted BySteven E Brenner