skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: SIFTER search: a web server for accurate phylogeny-based protein function prediction

Abstract

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. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

Authors:
 [1];  [1];  [1]
  1. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1257375
Grant/Contract Number:  
AC02-05CH11231; NIH R01 GM071749
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 43; Journal Issue: W1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats

Sahraeian, Sayed M., Luo, Kevin R., and Brenner, Steven E. SIFTER search: a web server for accurate phylogeny-based protein function prediction. United States: N. p., 2015. Web. doi:10.1093/nar/gkv461.
Sahraeian, Sayed M., Luo, Kevin R., & Brenner, Steven E. SIFTER search: a web server for accurate phylogeny-based protein function prediction. United States. doi:10.1093/nar/gkv461.
Sahraeian, Sayed M., Luo, Kevin R., and Brenner, Steven E. Fri . "SIFTER search: a web server for accurate phylogeny-based protein function prediction". United States. doi:10.1093/nar/gkv461. https://www.osti.gov/servlets/purl/1257375.
@article{osti_1257375,
title = {SIFTER search: a web server for accurate phylogeny-based protein function prediction},
author = {Sahraeian, Sayed M. and Luo, Kevin R. and Brenner, Steven E.},
abstractNote = {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. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.},
doi = {10.1093/nar/gkv461},
journal = {Nucleic Acids Research},
number = W1,
volume = 43,
place = {United States},
year = {2015},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

ConFunc—functional annotation in the twilight zone
journal, February 2008


Enhanced automated function prediction using distantly related sequences and contextual association by PFP
journal, June 2006

  • Hawkins, Troy; Luban, Stanislav; Kihara, Daisuke
  • Protein Science, Vol. 15, Issue 6
  • DOI: 10.1110/ps.062153506

Analysis of protein function and its prediction from amino acid sequence
journal, April 2011

  • Clark, Wyatt T.; Radivojac, Predrag
  • Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 7
  • DOI: 10.1002/prot.23029

Automated prediction of protein function and detection of functional sites from structure
journal, September 2004

  • Pazos, F.; Sternberg, M. J. E.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 41
  • DOI: 10.1073/pnas.0404569101

Inference of Protein Function from Protein Structure
journal, January 2005


Protein Molecular Function Prediction by Bayesian Phylogenomics
journal, January 2005

  • Engelhardt, Barbara E.; Jordan, Michael I.; Muratore, Kathryn E.
  • PLoS Computational Biology, Vol. 1, Issue 5
  • DOI: 10.1371/journal.pcbi.0010045

Genome-scale phylogenetic function annotation of large and diverse protein families
journal, July 2011

  • Engelhardt, B. E.; Jordan, M. I.; Srouji, J. R.
  • Genome Research, Vol. 21, Issue 11
  • DOI: 10.1101/gr.104687.109

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium
journal, August 2011

  • Gaudet, P.; Livstone, M. S.; Lewis, S. E.
  • Briefings in Bioinformatics, Vol. 12, Issue 5
  • DOI: 10.1093/bib/bbr042

Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
journal, March 1998


Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
journal, April 2006


Global protein function prediction from protein-protein interaction networks
journal, May 2003

  • Vazquez, Alexei; Flammini, Alessandro; Maritan, Amos
  • Nature Biotechnology, Vol. 21, Issue 6
  • DOI: 10.1038/nbt825

Prediction of Protein Function Using Protein–Protein Interaction Data
journal, December 2003


Predicting protein function from protein/protein interaction data: a probabilistic approach
journal, July 2003


Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
journal, June 2005


Network‐based prediction of protein function
journal, January 2007

  • Sharan, Roded; Ulitsky, Igor; Shamir, Ron
  • Molecular Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1038/msb4100129

Combining many interaction networks to predict gene function and analyze gene lists
journal, May 2012


Scale-space measures for graph topology link protein network architecture to function
journal, June 2014


New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
journal, June 2014


Predicting gene function in a hierarchical context with an ensemble of classifiers
journal, January 2008

  • Guan, Yuanfang; Myers, Chad L.; Hess, David C.
  • Genome Biology, Vol. 9, Issue Suppl 1
  • DOI: 10.1186/gb-2008-9-s1-s3

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae )
journal, June 2003

  • Troyanskaya, Olga G.; Dolinski, Kara; Owen, Art B.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 14
  • DOI: 10.1073/pnas.0832373100

Consistent probabilistic outputs for protein function prediction
journal, January 2008

  • Obozinski, Guillaume; Lanckriet, Gert; Grant, Charles
  • Genome Biology, Vol. 9, Issue Suppl 1
  • DOI: 10.1186/gb-2008-9-s1-s6

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
journal, January 2009

  • Costello, James C.; Dalkilic, Mehmet M.; Beason, Scott M.
  • Genome Biology, Vol. 10, Issue 9
  • DOI: 10.1186/gb-2009-10-9-r97

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
journal, February 2010


CombFunc: predicting protein function using heterogeneous data sources
journal, May 2012

  • Wass, Mark N.; Barton, Geraint; Sternberg, Michael J. E.
  • Nucleic Acids Research, Vol. 40, Issue W1
  • DOI: 10.1093/nar/gks489

A Probabilistic Functional Network of Yeast Genes
journal, November 2004


Basic Local Alignment Search Tool
journal, October 1990


A large-scale evaluation of computational protein function prediction
journal, January 2013

  • Radivojac, Predrag; Clark, Wyatt T.; Oron, Tal Ronnen
  • Nature Methods, Vol. 10, Issue 3
  • DOI: 10.1038/nmeth.2340

Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)
journal, August 2008


Pfam: the protein families database
journal, November 2013

  • Finn, Robert D.; Bateman, Alex; Clements, Jody
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1223

Errors in genome annotation
journal, April 1999


Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

BLAST: a more efficient report with usability improvements
journal, April 2013

  • Boratyn, Grzegorz M.; Camacho, Christiam; Cooper, Peter S.
  • Nucleic Acids Research, Vol. 41, Issue W1
  • DOI: 10.1093/nar/gkt282

The GOA database in 2009--an integrated Gene Ontology Annotation resource
journal, January 2009

  • Barrell, D.; Dimmer, E.; Huntley, R. P.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn803

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
journal, April 2009

  • Price, M. N.; Dehal, P. S.; Arkin, A. P.
  • Molecular Biology and Evolution, Vol. 26, Issue 7
  • DOI: 10.1093/molbev/msp077

    Works referencing / citing this record:

    NetGO: improving large-scale protein function prediction with massive network information
    journal, May 2019

    • You, Ronghui; Yao, Shuwei; Xiong, Yi
    • Nucleic Acids Research, Vol. 47, Issue W1
    • DOI: 10.1093/nar/gkz388