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References

thibaudnis edited this page Nov 8, 2019 · 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-2+

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
Lomsadze A, Gemayel K, Tang S, Borodovsky M.
Genome Research. 2018; 28(7):1079-1089.

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.

RFAMs

Rfam 12.0: updates to the RNA families database
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.
Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.

PILERCR

PILER-CR: fast and accurate identification of CRISPR repeats
Edgar RC.
BMC Bioinformatics. 2007 Jan 20;8:18.

CRSIPER Recognition Tool (CRT)

CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P.
BMC Bioinformatics. 2007 Jun 18;8:209.

tRNAscan-SE

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences
Chan PP, Lowe TM.
Methods Mol Biol. 2019;1962:1-14. doi: 10.1007/978-1-4939-9173-0_1

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