PATtyFams: Protein families for the microbial genomes in the PATRIC database

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Yoo, Hyunseung

doi:10.3389/fmicb.2016.00118

Title: PATtyFams: Protein families for the microbial genomes in the PATRIC database

Abstract

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.

Authors:

Davis, James J. ^[1]; Gerdes, Svetlana ^[2]; Olsen, Gary J. ^[3]; Olson, Robert ^[1]; Pusch, Gordon D. ^[2]; Shukla, Maulik ^[1]; Vonstein, Veronika ^[2]; Wattam, Alice R. ^[4]; Yoo, Hyunseung ^[1]

Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg,VA (United States)

Publication Date:: 2016-02-08

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1248167

Grant/Contract Number:: AC02-06CH11357; NNA13AA91A

Resource Type:: Accepted Manuscript

Journal Name:: Frontiers in Microbiology

Additional Journal Information:: Journal Volume: 7; Journal ID: ISSN 1664-302X

Publisher:: Frontiers Research Foundation

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; genome annotation; comparative genomics; metabolic modeling; FIGfams; RAST

Citation Formats


                    Davis, James J., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., and Yoo, Hyunseung. PATtyFams: Protein families for the microbial genomes in the PATRIC database.  United States: N. p., 2016. 
Web.  doi:10.3389/fmicb.2016.00118.

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                    Davis, James J., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., & Yoo, Hyunseung. PATtyFams: Protein families for the microbial genomes in the PATRIC database.  United States.  https://doi.org/10.3389/fmicb.2016.00118

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                    Davis, James J., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., and Yoo, Hyunseung. Mon .  
"PATtyFams: Protein families for the microbial genomes in the PATRIC database".  United States.  https://doi.org/10.3389/fmicb.2016.00118.  https://www.osti.gov/servlets/purl/1248167.

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@article{osti_1248167,

  title        = {PATtyFams: Protein families for the microbial genomes in the PATRIC database},

  author       = {Davis, James J. and Gerdes, Svetlana and Olsen, Gary J. and Olson, Robert and Pusch, Gordon D. and Shukla, Maulik and Vonstein, Veronika and Wattam, Alice R. and Yoo, Hyunseung},

  abstractNote = {The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.},

  doi          = {10.3389/fmicb.2016.00118},

  journal      = {Frontiers in Microbiology},

  number       = ,

  volume       = 7,

  place        = {United States},

  year         = {2016},

  month        = {2}

}

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Title: PATtyFams: Protein families for the microbial genomes in the PATRIC database

Abstract

Citation Formats

The RAST Server: Rapid Annotations using Subsystems Technology journal, January 2008

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models journal, October 2014

GenBank journal, November 2012

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) journal, May 2002

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal, February 2015

BLAST+: architecture and applications journal, January 2009

Toward Automatic Reconstruction of a Highly Resolved Tree of Life journal, March 2006

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Measures of the Amount of Ecologic Association Between Species journal, July 1945

Search and clustering orders of magnitude faster than BLAST journal, August 2010

Real Time Metagenomics: Using k-mers to annotate metagenomes journal, October 2012

An efficient algorithm for large-scale detection of protein families journal, April 2002

Enabling comparative modeling of closely related genomes: example genus Brucella journal, March 2014

Expanded microbial genome coverage and improved protein family annotation in the COG database journal, November 2014

TIGRFAMs and Genome Properties in 2013 journal, November 2012

Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach journal, December 2011

kClust: fast and sensitive clustering of large protein sequence databases journal, January 2013

High-throughput generation, optimization and analysis of genome-scale metabolic models journal, August 2010

Selection of representative protein data sets journal, March 1992

Genome Sequences of the Primary Endosymbiont “Candidatus Portiera aleyrodidarum” in the Whitefly Bemisia tabaci B and Q Biotypes journal, November 2012

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes journal, September 2003

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences journal, May 2006

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs journal, December 2011

CDD: NCBI's conserved domain database journal, November 2014

FIGfams: yet another set of protein families journal, September 2009

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees journal, November 2012

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes journal, September 2005

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal, November 2013

Databases of homologous gene families for comparative genomics journal, January 2009

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 journal, January 2001

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal, March 2010

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Automatic clustering of orthologs and in-paralogs from pairwise species comparisons journal, December 2001

Twilight zone of protein sequence alignments journal, February 1999

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RefSeq microbial genomes database: new representation and annotation strategy journal, December 2013

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome" journal, September 2005

PATRIC, the bacterial bioinformatics database and analysis resource journal, November 2013

Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence journal, December 2013

RefSeq microbial genomes database: new representation and annotation strategy journal, March 2015

Fully automatic 3D segmentation of the thoracolumbar spinal cord and the vertebral canal from T2-weighted MRI using K-means clustering algorithm journal, March 2020

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander journal, April 2020

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae journal, March 2021

Database resources of the National Center for Biotechnology Information journal, January 2006

Database resources of the National Center for Biotechnology Information journal, October 2020

Database resources of the National Center for Biotechnology Information journal, December 2007

Database resources of the National Center for Biotechnology Information journal, November 2018

Database resources of the National Center for Biotechnology Information journal, January 2009

Putative virulence factors of Plesiomonas shigelloides journal, August 2019

PATRIC as a unique resource for studying antimicrobial resistance journal, July 2017

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center journal, November 2016

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities journal, October 2019

Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii journal, October 2019

Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina journal, July 2019

Trait-based analysis of the human skin microbiome journal, July 2019

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico journal, October 2018

Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors journal, January 2020

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts text, January 2017

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes journal, October 2019

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts journal, March 2017

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier journal, October 2019

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
journal, October 2014

GenBank
journal, November 2012

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
journal, May 2002

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
journal, February 2015

BLAST+: architecture and applications
journal, January 2009

Toward Automatic Reconstruction of a Highly Resolved Tree of Life
journal, March 2006

In search of genome annotation consistency: solid gene clusters and how to use them
journal, July 2013

Measures of the Amount of Ecologic Association Between Species
journal, July 1945

Search and clustering orders of magnitude faster than BLAST
journal, August 2010

Real Time Metagenomics: Using k-mers to annotate metagenomes
journal, October 2012

An efficient algorithm for large-scale detection of protein families
journal, April 2002

Enabling comparative modeling of closely related genomes: example genus Brucella
journal, March 2014

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

TIGRFAMs and Genome Properties in 2013
journal, November 2012

Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach
journal, December 2011

kClust: fast and sensitive clustering of large protein sequence databases
journal, January 2013

High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

Selection of representative protein data sets
journal, March 1992

Genome Sequences of the Primary Endosymbiont “Candidatus Portiera aleyrodidarum” in the Whitefly Bemisia tabaci B and Q Biotypes
journal, November 2012

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
journal, May 2006

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
journal, December 2011

CDD: NCBI's conserved domain database
journal, November 2014

FIGfams: yet another set of protein families
journal, September 2009

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
journal, November 2012

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

Databases of homologous gene families for comparative genomics
journal, January 2009

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
journal, January 2001

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010

The Pfam protein families database
journal, November 2011

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
journal, December 2001

Twilight zone of protein sequence alignments
journal, February 1999

Database resources of the National Center for Biotechnology Information
journal, May 2009

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
journal, June 2014

The history of the genetic sequence databases
journal, April 1990

RefSeq microbial genomes database: new representation and annotation strategy
journal, December 2013

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome"
journal, September 2005

PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013

Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence
journal, December 2013

RefSeq microbial genomes database: new representation and annotation strategy
journal, March 2015

Fully automatic 3D segmentation of the thoracolumbar spinal cord and the vertebral canal from T2-weighted MRI using K-means clustering algorithm
journal, March 2020

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
journal, April 2020

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae
journal, March 2021

Database resources of the National Center for Biotechnology Information
journal, January 2006

Database resources of the National Center for Biotechnology Information
journal, October 2020

Database resources of the National Center for Biotechnology Information
journal, December 2007

Database resources of the National Center for Biotechnology Information
journal, November 2018

Database resources of the National Center for Biotechnology Information
journal, January 2009

Putative virulence factors of Plesiomonas shigelloides
journal, August 2019

PATRIC as a unique resource for studying antimicrobial resistance
journal, July 2017

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
journal, November 2016

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
journal, October 2019

Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
journal, October 2019

Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina
journal, July 2019

Trait-based analysis of the human skin microbiome
journal, July 2019

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico
journal, October 2018

Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors
journal, January 2020

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts
text, January 2017

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes
journal, October 2019

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts
journal, March 2017

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier
journal, October 2019