ProGenomes: A resource for consistent functional and taxonomic annotations of prokaryotic genomes

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D529-D534

  Mende, Daniel R ^a,b   Letunic, Ivica ^c   Huerta Cepas, Jaime ^a   Li, Simone S ^a,d   Forslund, Kristoffer ^a   Sunagawa, Shinichi ^a,e   Bork, Peer ^a,f,g,h  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF HAWAII   (United States)

^c biobyte solutions GmbH   (Germany)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

^e ETH ZURICH   (Switzerland)

^f UNIVERSITY OF HEIDELBERG   (Germany)

^g MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^h UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE;

ARTICLE; CLADISTICS; CONTROLLED STUDY; DATA BASE; GENE SEQUENCE; GENETIC CODE; HABITAT; MICROBIAL COMMUNITY; MICROBIAL GENOME; MICROBIOLOGY; MICROORGANISM; NONHUMAN; PHENOTYPE; PROGENOMES DATABASE; SEQUENCE ALIGNMENT; BIOLOGY; DNA BARCODING; GENETIC DATABASE; GENOME; GENOMICS; MOLECULAR GENETICS; PROCEDURES; PROKARYOTIC CELL; WEB BROWSER;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA BARCODING, TAXONOMIC; GENOME; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; PROKARYOTIC CELLS; WEB BROWSER;

EID: 85016118733     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw989     Document Type: Article

References (28)

1. Hall,N. (2007) Advanced sequencing technologies and their wider impact in microbiology. J.Exp. Biol., 210, 1518-1525.
2. Fleischmann,R.D., Adams,M.D., White,O., Clayton,R.A., Kirkness,E.F., Kerlavage,A.R., Bult,C.J., Tomb,J.F., Dougherty,B.A. and Merrick,J.M. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
3. Fraser,C.M., Gocayne,J.D.,White,O., Adams,M.D., Clayton,R.A., Fleischmann,R.D., Bult,C.J., Kerlavage,A.R., Sutton,G., Kelley,J.M. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
4. Overbeek,R., Olson,R., Pusch,G.D., Olsen,G.J., Davis,J.J., Disz,T., Edwards,R.A., Gerdes,S., Parrello,B., Shukla,M. et al. (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res., 42, D206-D214.
5. Medini,D., Duccio,M., Davide,S., Julian,P., Relman,D.A., Claudio,D., Richard,M., Stanley,F. and Rino,R. (2008) Microbiology in the post-genomic era. Nat. Rev. Microbiol., 6, 419-430.
6. Tatusova,T., Ciufo,S., Federhen,S., Fedorov,B., McVeigh,R., O'Neill,K., Tolstoy,I. and Zaslavsky,L. (2014) Update on RefSeq microbial genomes resources. Nucleic Acids Res., 43, D599-D605.
7. Markowitz,V.M., Chen,I.-M.A., Palaniappan,K., Chu,K., Szeto,E., Pillay,M., Ratner,A., Huang,J., Woyke,T., Huntemann,M. et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res., 42, D560-D567.
8. Wattam,A.R., Abraham,D., Dalay,O., Disz,T.L., Driscoll,T., Gabbard,J.L., Gillespie,J.J., Gough,R., Hix,D., Kenyon,R. et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591.
9. Kersey,P.J., Allen,J.E., Armean,I., Boddu,S., Bolt,B.J., Carvalho-Silva,D., Christensen,M., Davis,P., Falin,L.J., Grabmueller,C. et al. (2016) Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Res., 44, D574-D580.
10. Rossell ó-Mora,R. and Amann,R. (2001) The species concept for prokaryotes. FEMS Microbiol. Rev., 25, 39-67.
11. Davis,J.J., Boisvert,S., Brettin,T., Kenyon,R.W.,Mao,C., Olson,R., Overbeek,R., Santerre,J., Shukla,M., Wattam,A.R. et al. (2016) Antimicrobial Resistance Prediction in PATRIC and RAST. Sci. Rep., 6, 27930.
12. Kanehisa,M., Minoru,K., Yoko,S., Masayuki,K., Miho,F. and Mao,T. (2015) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res., 44, D457-D462.
13. Mende,D.R., Sunagawa,S., Zeller,G. and Bork,P. (2013) Accurate and universal delineation of prokaryotic species. Nat. Methods, 10, 881-884.
14. Huerta-Cepas,J., Jaime,H.-C., Damian,S., Kristoffer,F., Helen,C., Davide,H.,Walter,M.C., Thomas,R., Mende,D.R., Shinichi,S. et al. (2015) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res., 44, D286-D293.
15. Huerta-Cepas,J., Forslund,K., Szklarczyk,D., Jensen,L.J., von Mering,C. and Bork,P. (2016) Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. bioRxiv, 76331, 1-11.
16. Borodovsky,M., Mark,B. and Alex,L. (2014) Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. Curr. Protoc. Microbiol., 32, doi:10.1002/0471250953.bi0405s35.
17. Ciccarelli,F.D., Doerks,T., von Mering,C., Creevey,C.J., Snel,B. and Bork,P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science, 311, 1283-1287.
18. Sorek,R., Zhu,Y., Creevey,C.J., Francino,M.P., Bork,P. and Rubin,E.M. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science, 318, 1449-1452.
19. Huang,K., Brady,A., Mahurkar,A.,White,O., Gevers,D., Huttenhower,C. and Segata,N. (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res., 42, D617-D624.
20. Minguez,P., Letunic,I., Parca,L., Garcia-Alonso,L., Dopazo,J., Huerta-Cepas,J. and Bork,P. (2015) PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res., 43, D494-D502.
21. Sunagawa,S., Mende,D.R., Zeller,G., Izquierdo-Carrasco,F., Berger,S.A., Kultima,J.R., Coelho,L.P., Arumugam,M., Tap,J., Nielsen,H.B. et al. (2013) Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods, 10, 1196-1199.
22. Schloissnig,S., Arumugam,M., Sunagawa,S., Mitreva,M., Tap,J., Zhu,A., Waller,A., Mende,D.R., Kultima,J.R., Martin,J. et al. (2013) Genomic variation landscape of the human gut microbiome. Nature, 493, 45-50.
23. McArthur,A.G., Waglechner,N., Nizam,F., Yan,A., Azad,M.A., Baylay,A.J., Bhullar,K., Canova,M.J., De Pascale,G., Ejim,L. et al. (2013) The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother., 57, 3348-3357.
24. Gibson,M.K., Forsberg,K.J. and Dantas,G. (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J., 9, 207-216.
25. Lombard,V., Vincent,L., Ramulu,H.G., Elodie,D., Coutinho,P.M. and Bernard,H. (2013) The carbohydrate-Active enzymes database (CAZy) in 2013. Nucleic Acids Res., 42, D490-D495.
26. Yin,Y., Mao,X., Yang,J., Chen,X., Mao,F. and Xu,Y. (2012) dbCAN: a web resource for automated carbohydrate-Active enzyme annotation. Nucleic Acids Res., 40, W445-W451.
27. Smillie,C.S., Smith,M.B., Friedman,J., Cordero,O.X., David,L.A. and Alm,E.J. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480, 241-244.
28. Letunic,I. and Bork,P. (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res., 44, W242-W245.