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References

cohenrf edited this page Oct 4, 2018 · 12 revisions

NCBI

NCBI prokaryotic genome annotation pipeline.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J.
Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. Epub 2016 Jun 24.

RefSeq: an update on prokaryotic genome annotation and curation.
Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD.
Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860.

GeneMarkS

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
Besemer J, Lomsadze A, Borodovsky M.
Nucleic Acids Research. 2001;29(12):2607-2618.

TIGRFAMs

TIGRFAMs: a protein family resource for the functional identification of proteins.
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O.
Nucleic Acids Res. 2001 Jan 1;29(1):41-3.

The TIGRFAMs database of protein families.
Haft DH, Selengut JD, White O.
Nucleic Acids Res. 2003 Jan 1;31(1):371-3.

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O.
Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4. Epub 2006 Dec 6.

TIGRFAMs and Genome Properties in 2013.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.
Nucleic Acids Res. 2013 Jan;41(Database issue):D387-95. doi: 10.1093/nar/gks1234. Epub 2012 Nov 28.

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