NCBI prokaryotic genome annotation pipeline

Nucleic Acids Research

Volumn 44, Issue 14, 2016, Pages 6614-6624

  Tatusova, Tatiana ^a   Dicuccio, Michael ^a   Badretdin, Azat ^a   Chetvernin, Vyacheslav ^a   Nawrocki, Eric P ^a   Zaslavsky, Leonid ^a   Lomsadze, Alexandre ^b   Pruitt, Kim D ^a   Borodovsky, Mark ^b,c   Ostell, James ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLADISTICS; CONTROLLED STUDY; GENE FREQUENCY; GENE SEQUENCE; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; MICROBIAL GENOME; MOLECULAR MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROKARYOTIC GENOME ANNOTATION PIPELINE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIVERSITY; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PROKARYOTIC CELL;

BACTERIAL PROTEIN;

BACTERIA; BACTERIAL PROTEINS; DATABASES, NUCLEIC ACID; GENES, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; PROKARYOTIC CELLS;

EID: 84984869357     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw569     Document Type: Article

References (36)

1. Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 26, 1107-1115.
2. Delcher,A.L., Harmon,D., Kasif,S., White,O. and Salzberg,S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 23, 4636-4641.
3. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
4. Klimke,W., Agarwala,R., Badretdin,A., Chetvernin,S., Ciufo,S., Fedorov,B., Kiryutin,B., O'Neill,K., Resch,W., Resenchuk,S. et al. (2009) The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res., 37, D216-D223.
5. Nawrocki,E.P. and Eddy,S.R. (2013) Infernal 1.1: 100-fold faster RNA Homology searches. Bioinformatics, 29, 2933-2935.
6. Nawrocki,E.P. (2014) Annotating functional RNAs in genomes using Infernal. Methods Mol. Biol., 1097, 163-197.
7. Nawrocki,E.P., Burge,S.W., Bateman,A., Daub,J., Eberhardt,R.Y., Eddy,S.R., Floden,E.W., Gardner,P.P., Jones,T.A., Tate,J. et al. (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., 43, D130-D138.
8. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
9. Angiuoli,S., Gussman,A., Klimke,W., Cochrane,G., Field,D., Garrity,G., Kodira,C.D., Kyrpides,N., Madupu,R., Markowitz,V. et al. (2008) Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS, 12, 137-141.
10. 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.
11. Seemann,T. (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30, 2068-2069.
12. Pati,A., Ivanova,N.N., Mikhailova,N., Ovchinnikova,G., Hooper,S.D., Lykidis,A. and Kyrpides,N.C. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat. Methods, 7, 455-457.
13. Pareja-Tobes,P., Manrique,M., Pareja-Tobes,E., Pareja,E. and Tobes,R. (2012) BG7: a new approach for bacterial genome annotation designed for next generation sequencing data. PLoS One, 7, e49239.
14. 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., Merrick,J.M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
15. Tettelin,H., Masignani,V., Cieslewicz,M.J., Donati,C., Medini,D., Ward,N.L., Angiuoli,S.V., J.,Crabtree., Jones,A.L., Durkin,A.S. et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc. Natl. Acad. Sci. U.S.A., 102, 13950-13955.
16. Mira,A., Martín-Cuadrado,A.B., D'Auria,G. and Rodrguez-Valera,F. (2010) The bacterial pan-genome: a new paradigm in microbiology. Int. Microbiol., 13, 45-57.
17. Zaslavsky,L., Ciufo,S., Fedorov,B., Kiryutin,B., Tolstoy,I. and Tatusova,T. (2016) Dealing with the data deluge: new strategies in prokaryotic genome analysis. In: Kulski,JK (ed.) Next Generation Sequencing-Advances, Applications and Challenges. InTech, Croatia.
18. Edgar,R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
19. Zaslavsky,L. and Tatusova,T. (2015) Clustering analysis of proteins from microbial genomes at multiple levels of resolution. In: Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015, June 7-10, Proceedings. Norfolk, pp. 438-440.
20. 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.
21. Mende,D.R., Sunagawa,S., Zeller,G. and Bork,P. (2013) Accurate and universal delineation of prokaryotic species. Nat. Methods, 10, 881-884.
22. Tatusova,T., Ciufo,S., Federhen,S., Fedorov,B., McVeigh,R., O'Neill,K., Tolstoy,I. and Zaslavsky,L. (2015) Update on RefSeq microbial genome resources. Nucleic Acids Res., 43, D599-D605.
23. Camacho,C., Coulouris,G., Avagyan,V.,Ma,N., Papadopoulos,J., Bealer,K. and Madden,T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
24. Grissa,I., Vergnaud,G. and Pourcel,C. (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics, 8, 172.
25. Makarova,K.S., Haft,D.H., Barrangou,R., Brouns,S.J., Charpentier,E., Horvath,P., Moineau,S., Mojica,F.J., Wolf,Y.I., Yakunin,A.F. et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol., 9, 467-467.
26. Bland,C., Ramsey,T.L., Sabree,F., Lowe,M., Brown,K., Kyrpides,N.C. and Hugenholtz,P. (2007) CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8, 209.
27. Biswas,A., Gagnon,J.N., Brouns,S.J., Fineran,P.C. and Brown,C.M. (2013) CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biol., 10, 817-827.
28. Lukashin,A.V. and Borodovsky,M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
29. UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
30. Klimke,W., O'Donovan,C., White,O., Brister,J.R., Clark,K., Fedorov,B., Mizrachi,I., Pruitt,K.D. and Tatusova,T. (2011) Solving the problem: Genome annotation standards before the data deluge. Stand. Genomic Sci., 5, 168-193.
31. Poptsova,M.S. and Gogarten,J.P. (2010) Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology, 156, 1909-1917.
32. Radivojac,P., Clark,W.T., Oron,T.R., Schnoes,A.M., Wittkop,T., Sokolov,A., Graim,K., Funk,C., Verspoor,K., Ben-Hur,A. et al. (2013) A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227.
33. Tatusova,T., Ciufo,S., Fedorov,B., O'Neill,K. and Tolstoy,I. (2014) RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res., 42, D553-D559.
34. Zhou,J., Richardson,A.J. and Rudd,K.E. (2013) EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes. Bioinformatics, 29, 1917-1918.
35. Lew,J.M., Mao,C., Shukla,M., Warren,A., Will,R., Kuznetsov,D., Xenarios,I., Robertson,B.D., Gordon,S.V., Schnappinger,D. et al. (2013) Database resources for the tuberculosis community. Tuberculosis (Edinb), 93, 12-17.
36. Winsor,G.L., Lam,D.K., Fleming,L., Lo,R., Whiteside,M.D., Yu,N.Y., Hancock,R.E. and Brinkman,F.S. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res., 39, D596-D600.