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

Journal Article · Mon Feb 08 00:00:00 EST 2016 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2016.00118· OSTI ID:1248167

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)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

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

OSTI ID:: 1248167

Journal Information:: Frontiers in Microbiology, Vol. 7; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 102 works

Citation information provided by
Web of Science

References (50)

The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S. PLoS Computational Biology, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pcbi.1003882	journal	October 2014
GenBank Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1195	journal	November 2012
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Bentley, S. D.; Chater, K. F.; Cerdeño-Tárraga, A. -M. Nature, Vol. 417, Issue 6885 https://doi.org/10.1038/417141a	journal	May 2002
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Brettin, Thomas; Davis, James J.; Disz, Terry Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08365	journal	February 2015
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Toward Automatic Reconstruction of a Highly Resolved Tree of Life Ciccarelli, F. D. Science, Vol. 311, Issue 5765 https://doi.org/10.1126/science.1123061	journal	March 2006
In search of genome annotation consistency: solid gene clusters and how to use them Davis, James J.; Olsen, Gary J.; Overbeek, Ross 3 Biotech, Vol. 4, Issue 3 https://doi.org/10.1007/s13205-013-0152-2	journal	July 2013
Measures of the Amount of Ecologic Association Between Species Dice, Lee R. Ecology, Vol. 26, Issue 3 https://doi.org/10.2307/1932409	journal	July 1945
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
Real Time Metagenomics: Using k-mers to annotate metagenomes Edwards, Robert A.; Olson, Robert; Disz, Terry Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts599	journal	October 2012
An efficient algorithm for large-scale detection of protein families Enright, A. J. Nucleic Acids Research, Vol. 30, Issue 7 https://doi.org/10.1093/nar/30.7.1575	journal	April 2002
Enabling comparative modeling of closely related genomes: example genus Brucella Faria, José P.; Edirisinghe, Janaka N.; Davis, James J. 3 Biotech, Vol. 5, Issue 1 https://doi.org/10.1007/s13205-014-0202-4	journal	March 2014
Expanded microbial genome coverage and improved protein family annotation in the COG database Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1223	journal	November 2014
TIGRFAMs and Genome Properties in 2013 Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1234	journal	November 2012
Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach Halachev, Mihail R.; Loman, Nicholas J.; Pallen, Mark J. PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0028388	journal	December 2011
kClust: fast and sensitive clustering of large protein sequence databases Hauser, Maria; Mayer, Christian E.; Söding, Johannes BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-248	journal	January 2013
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
Selection of representative protein data sets Hobohm, Uwe; Scharf, Michael; Schneider, Reinhard Protein Science, Vol. 1, Issue 3 https://doi.org/10.1002/pro.5560010313	journal	March 1992
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Li, L. Genome Research, Vol. 13, Issue 9 https://doi.org/10.1101/gr.1224503	journal	September 2003
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs Mahmood, Khalid; Webb, Geoffrey I.; Song, Jiangning Nucleic Acids Research, Vol. 40, Issue 6 https://doi.org/10.1093/nar/gkr1261	journal	December 2011
CDD: NCBI's conserved domain database Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1221	journal	November 2014
FIGfams: yet another set of protein families Meyer, Folker; Overbeek, Ross; Rodriguez, Alex Nucleic Acids Research, Vol. 37, Issue 20 https://doi.org/10.1093/nar/gkp698	journal	September 2009
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees Mi, Huaiyu; Muruganujan, Anushya; Thomas, Paul D. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1118	journal	November 2012
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 Perna, Nicole T.; Plunkett, Guy; Burland, Valerie Nature, Vol. 409, Issue 6819 https://doi.org/10.1038/35054089	journal	January 2001
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
The Pfam protein families database Punta, M.; Coggill, P. C.; Eberhardt, R. Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1065	journal	November 2011
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons Remm, Maido; Storm, Christian E. V.; Sonnhammer, Erik L. L. Journal of Molecular Biology, Vol. 314, Issue 5 https://doi.org/10.1006/jmbi.2000.5197	journal	December 2001
Twilight zone of protein sequence alignments Rost, Burkhard Protein Engineering, Design and Selection, Vol. 12, Issue 2 https://doi.org/10.1093/protein/12.2.85	journal	February 1999
Database resources of the National Center for Biotechnology Information Sayers, E. W.; Barrett, T.; Benson, D. A. Nucleic Acids Research, Vol. 37, Issue 9 https://doi.org/10.1093/nar/gkp382	journal	May 2009
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane Proceedings of the National Academy of Sciences, Vol. 111, Issue 26 https://doi.org/10.1073/pnas.1401329111	journal	June 2014
The history of the genetic sequence databases Smith, Temple F. Genomics, Vol. 6, Issue 4 https://doi.org/10.1016/0888-7543(90)90509-S	journal	April 1990
RefSeq microbial genomes database: new representation and annotation strategy Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1274	journal	December 2013
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome" Tettelin, H.; Masignani, V.; Cieslewicz, M. J. Proceedings of the National Academy of Sciences, Vol. 102, Issue 39 https://doi.org/10.1073/pnas.0506758102	journal	September 2005
PATRIC, the bacterial bioinformatics database and analysis resource Wattam, Alice R.; Abraham, David; Dalay, Oral Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1099	journal	November 2013
RefSeq microbial genomes database: new representation and annotation strategy Tatusova, T.; Ciufo, S.; Fedorov, B. Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv278	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 Sabaghian, Sahar; Dehghani, Hamed; Batouli, Seyed Amir Hossein Spinal Cord, Vol. 58, Issue 7 https://doi.org/10.1038/s41393-020-0429-3	journal	March 2020
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander Song, Xiaoming; Nie, Fulei; Chen, Wei Horticulture Research, Vol. 7, Issue 1 https://doi.org/10.1038/s41438-020-0261-0	journal	April 2020
Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae Will, Robert C.; Ramamurthy, Thandavarayan; Sharma, Naresh Chand Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21870-5	journal	March 2021
Database resources of the National Center for Biotechnology Information Wheeler, D. L. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj158	journal	January 2006
Database resources of the National Center for Biotechnology Information Sayers, Eric W.; Beck, Jeffrey; Bolton, Evan E. Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa892	journal	October 2020
Database resources of the National Center for Biotechnology Information Wheeler, D. L.; Barrett, T.; Benson, D. A. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm1000	journal	December 2007
Database resources of the National Center for Biotechnology Information Sayers, Eric W.; Agarwala, Richa; Bolton, Evan E. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1069	journal	November 2018
Database resources of the National Center for Biotechnology Information Sayers, E. W.; Barrett, T.; Benson, D. A. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn741	journal	January 2009
Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence Wattam, A. R.; Foster, J. T.; Mane, S. P. Journal of Bacteriology, Vol. 196, Issue 5 https://doi.org/10.1128/jb.01091-13	journal	December 2013
Genome Sequences of the Primary Endosymbiont “Candidatus Portiera aleyrodidarum” in the Whitefly Bemisia tabaci B and Q Biotypes Jiang, Zi-Feng; Xia, Fangfang; Johnson, Kipp W. Journal of Bacteriology, Vol. 194, Issue 23 https://doi.org/10.1128/jb.01841-12	journal	November 2012
Databases of homologous gene families for comparative genomics Penel, Simon; Arigon, Anne-Muriel; Dufayard, Jean-François BMC Bioinformatics, Vol. 10, Issue Suppl 6 https://doi.org/10.1186/1471-2105-10-s6-s3	journal	January 2009

Cited By (17)

Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center Wattam, Alice R.; Brettin, Thomas; Davis, James J. Comparative Genomics https://doi.org/10.1007/978-1-4939-7463-4_4	book	December 2017
Putative virulence factors of Plesiomonas shigelloides Edwards, Melissa S.; McLaughlin, Richard William; Li, Jia Antonie van Leeuwenhoek, Vol. 112, Issue 12 https://doi.org/10.1007/s10482-019-01303-6	journal	August 2019
PATRIC as a unique resource for studying antimicrobial resistance Antonopoulos, Dionysios A.; Assaf, Rida; Aziz, Ramy Karam Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx083	journal	July 2017
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center Wattam, Alice R.; Davis, James J.; Assaf, Rida Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1017	journal	November 2016
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities Davis, James J.; Wattam, Alice R.; Aziz, Ramy K. Nucleic Acids Research https://doi.org/10.1093/nar/gkz943	journal	October 2019
SwiftOrtho: a Fast, Memory-Efficient, Multiple Genome Orthology Classifier Hu, Xiao; Friedberg, Iddo GigaScience https://doi.org/10.1101/543223	journal	February 2019
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii Ruiz, Cristian; McCarley, Ashley; Espejo, Manuel Luis mSphere, Vol. 4, Issue 5 https://doi.org/10.1128/msphere.00631-19	journal	October 2019
Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina Gagetti, Paula; Wattam, Alice R.; Giacoboni, Gabriela BMC Veterinary Research, Vol. 15, Issue 1 https://doi.org/10.1186/s12917-019-1990-x	journal	July 2019
Trait-based analysis of the human skin microbiome Bewick, Sharon; Gurarie, Eliezer; Weissman, Jake L. Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0698-2	journal	July 2019
First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico Parise, Doglas; Parise, Mariana T. D.; Viana, Marcus V. C. Standards in Genomic Sciences, Vol. 13, Issue 1 https://doi.org/10.1186/s40793-018-0325-z	journal	October 2018
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors Susič, Nik; Janežič, Sandra; Rupnik, Maja G3: Genes\|Genomes\|Genetics, Vol. 10, Issue 3 https://doi.org/10.1534/g3.119.400716	journal	January 2020
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts Al Dahouk, Sascha; Köhler, Stephan; Occhialini, Alessandra RWTH Aachen University https://doi.org/10.18154/rwth-conv-221967	text	January 2017
A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes Deo, Dipti; Davray, Dimple; Kulkarni, Ram Microorganisms, Vol. 7, Issue 10 https://doi.org/10.3390/microorganisms7100444	journal	October 2019
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts Al Dahouk, Sascha; Köhler, Stephan; Occhialini, Alessandra Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep44420	journal	March 2017
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier Hu, Xiao; Friedberg, Iddo GigaScience, Vol. 8, Issue 10 https://doi.org/10.1093/gigascience/giz118	journal	October 2019
Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar Rabenandrasana, Mamitina Alain Noah; Rafetrarivony, Lala Fanomezantsoa; Rivoarilala, Lalainasoa Odile Microbiology Resource Announcements, Vol. 8, Issue 35 https://doi.org/10.1128/mra.00752-19	journal	August 2019
Corrigendum G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 9, p. 3465-3465 https://doi.org/10.1534/g3.120.401609	journal	September 2020

Similar Records

PATRIC, the bacterial bioinformatics database and analysis resource

Journal Article · Tue Nov 12 00:00:00 EST 2013 · Nucleic Acids Research · OSTI ID:1248167

Wattam, Alice R.; Abraham, David; Dalay, Oral; +25 more

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

Journal Article · Mon Nov 28 00:00:00 EST 2016 · Nucleic Acids Research · OSTI ID:1248167

Davis, James J.; Brettin, Thomas; Dietrich, Emily M.; +11 more

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

Journal Article · Thu Oct 31 00:00:00 EDT 2019 · Nucleic Acids Research · OSTI ID:1248167

Davis, James J.; Wattam, Alice R.; Aziz, Ramy K.; +31 more

Related Subjects

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

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

Citation Formats

References (50)

Cited By (17)

Similar Records

Related Subjects