title: Bioinformatics of prokaryotic RNAs.
abstract: The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes.
authors.affiliation: Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany; Center for non-coding RNA in Technology and Health; University of Copenhagen; Grønnegårdsvej 3; DK-1870 Frederiksberg C, Denmark.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.affiliation: Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria; Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Härtelstraße 16-18; D-04107 Leipzig, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Amman
authors.affiliation: Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Costa
authors.affiliation: Bioinformatics and Computational Biology Research Group; University of Vienna; Währingerstraße 29; A-1090 Wien, Austria; Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria.
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiß
authors.affiliation: Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany; Max Planck Institute of Immunobiology and Epigenetics; Stübeweg 51; D-79108 Freiburg, Germany.
authors.forename: Andreas S
authors.initials: AS
authors.lastname: Richter
authors.affiliation: Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria; Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Härtelstraße 16-18; D-04107 Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences; Inselstraße 22; D-04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology - IZI; Perlickstraße 1; D-04103 Leipzig, Germany; Center for non-coding RNA in Technology and Health; University of Copenhagen; Grønnegårdsvej 3; DK-1870 Frederiksberg C, Denmark; Santa Fe Institute; Santa Fe, NM USA.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D020029:Base Pairing; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D023281:Genomics; D009690:Nucleic Acid Conformation; D011387:Prokaryotic Cells / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: RNA bioinformatics; RNA–RNA interaction; TSS annotation; gene finding; secondary structure prediction; target prediction
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
references.pmid: 15980540
references.citation: J Bacteriol. 1988 Jan;170(1):155-62
references.pmid: 2447060
references.citation: Genome Biol. 2007;8(2):R22
references.pmid: 17313685
references.citation: Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998-9002
references.pmid: 2461560
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W107-11
references.pmid: 21609960
references.citation: Nucleic Acids Res. 2012 Nov;40(21):10964-79
references.pmid: 22965121
references.citation: J Math Biol. 2008 Jan;56(1-2):129-44
references.pmid: 17611759
references.citation: BMC Bioinformatics. 2001;2:8
references.pmid: 11801179
references.citation: Microbiology (Reading). 2008 Oct;154(Pt 10):3175-3187
references.pmid: 18832323
references.citation: Bioinformatics. 2007 Apr 15;23(8):926-32
references.pmid: 17324941
references.citation: RNA. 2004 Oct;10(10):1507-17
references.pmid: 15383676
references.citation: Nature. 2010 Mar 11;464(7286):250-5
references.pmid: 20164839
references.citation: Bioinformatics. 2011 Apr 15;27(8):1076-85
references.pmid: 21335320
references.citation: Bioinformatics. 2009 Oct 15;25(20):2646-54
references.pmid: 19671692
references.citation: Methods Mol Biol. 2012;905:99-122
references.pmid: 22736001
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5
references.pmid: 21062808
references.citation: RNA. 2006 Mar;12(3):323-31
references.pmid: 16495231
references.citation: Algorithms Mol Biol. 2011 Nov 24;6:26
references.pmid: 22115189
references.citation: Bioinformatics. 2011 Jul 15;27(14):1934-40
references.pmid: 21593134
references.citation: Bioinformatics. 2014 Jul 1;30(13):1837-43
references.pmid: 24626854
references.citation: Comput Syst Bioinformatics Conf. 2006;:111-21
references.pmid: 17369630
references.citation: Biol Chem. 2011 Apr;392(4):305-13
references.pmid: 21345160
references.citation: PLoS Genet. 2007 Dec;3(12):e229
references.pmid: 18159946
references.citation: Nucleic Acids Res. 2005 Apr 28;33(8):2433-9
references.pmid: 15860779
references.citation: J Mol Biol. 2005 Feb 4;345(5):987-1001
references.pmid: 15644199
references.citation: Bioinformatics. 2010 Jan 15;26(2):175-81
references.pmid: 19910305
references.citation: Biophys J. 2004 Jul;87(1):215-26
references.pmid: 15240459
references.citation: BMC Genomics. 2014 Apr 05;15:264
references.pmid: 24708189
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D205-9
references.pmid: 21984475
references.citation: J Comput Biol. 2010 Mar;17(3):429-42
references.pmid: 20377455
references.citation: BMC Bioinformatics. 2007 Apr 19;8:130
references.pmid: 17445273
references.citation: Genome Inform. 2004;15(2):92-101
references.pmid: 15706495
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W368-72
references.pmid: 20501603
references.citation: Genome Biol. 2014 Feb 10;15(2):R34
references.pmid: 24512684
references.citation: Nucleic Acids Res. 1994 Jun 11;22(11):2079-88
references.pmid: 8029015
references.citation: Nucleic Acids Res. 2013 Sep;41(17):8034-44
references.pmid: 23863837
references.citation: BMC Bioinformatics. 2008 Feb 26;9:122
references.pmid: 18302738
references.citation: RNA Biol. 2012 Dec;9(12):1399-404
references.pmid: 23324554
references.citation: Nat Rev Microbiol. 2012 Mar 16;10(4):255-65
references.pmid: 22421878
references.citation: Nucleic Acids Res. 2004 Sep 24;32(16):4925-36
references.pmid: 15448187
references.citation: Bioinformatics. 2012 Jun 15;28(12):i224-32
references.pmid: 22689765
references.citation: J Bacteriol. 2011 Apr;193(7):1690-701
references.pmid: 21278294
references.citation: Nucleic Acids Res. 2004 Sep 15;32(16):4843-51
references.pmid: 15371549
references.citation: Genome Res. 2007 Jan;17(1):117-25
references.pmid: 17151342
references.citation: PLoS Pathog. 2013 Sep;9(9):e1003626
references.pmid: 24068933
references.citation: Proc Natl Acad Sci U S A. 2012 May 15;109(20):E1277-86
references.pmid: 22538806
references.citation: Nucleic Acids Res. 2012 May;40(10):4261-72
references.pmid: 22287623
references.citation: Nucleic Acids Res. 2012 Jul;40(12):5215-26
references.pmid: 22373926
references.citation: Mol Microbiol. 2007 Dec;66(5):1080-91
references.pmid: 17971083
references.citation: Mol Cell. 2011 Sep 16;43(6):867-79
references.pmid: 21925376
references.citation: J Proteomics. 2013 Jun 28;86:27-42
references.pmid: 23665149
references.citation: RNA Biol. 2012 Feb;9(2):119-29
references.pmid: 22418845
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503
references.pmid: 23503844
references.citation: Nucleic Acids Res. 2005 Jul 26;33(13):4096-105
references.pmid: 16049021
references.citation: Curr Protoc Bioinformatics. 2009 Jun;Chapter 12:12.8.1-12.8.17
references.pmid: 19496058
references.citation: Nucleic Acids Res. 2012 Mar;40(5):2020-31
references.pmid: 22080557
references.citation: Nucleic Acids Res. 2011 Aug;39(14):e93
references.pmid: 21593129
references.citation: Genes Dev. 2007 Jun 1;21(11):1353-66
references.pmid: 17545468
references.citation: RNA Biol. 2009 Jul-Aug;6(3):222-7
references.pmid: 19502815
references.citation: Nat Rev Microbiol. 2011 Aug 15;9(8):578-89
references.pmid: 21760622
references.citation: Nucleic Acids Res. 1981 Jan 10;9(1):133-48
references.pmid: 6163133
references.citation: J Comput Biol. 2006 Mar;13(2):267-82
references.pmid: 16597239
references.citation: Bioinformatics. 2011 Jan 15;27(2):211-9
references.pmid: 21088024
references.citation: Bioinformatics. 2011 Oct 15;27(20):2790-6
references.pmid: 21856737
references.citation: Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):397-401
references.pmid: 8552647
references.citation: Nat Methods. 2013 Dec;10(12):1185-91
references.pmid: 24185836
references.citation: Bioinformatics. 2012 Nov 1;28(21):2738-46
references.pmid: 22923300
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Methods. 2010 Oct;52(2):150-8
references.pmid: 20554050
references.citation: Bioinformatics. 2009 Jun 15;25(12):i365-73
references.pmid: 19478011
references.citation: Pac Symp Biocomput. 2010;:69-79
references.pmid: 19908359
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W149-54
references.pmid: 21672960
references.citation: J Comput Biol. 2012 Jun;19(6):796-813
references.pmid: 22506536
references.citation: Nucleic Acids Res. 2009 Apr;37(5):1602-15
references.pmid: 19151082
references.citation: Nucleic Acids Res. 2011 Sep 1;39(16):6886-95
references.pmid: 21624887
references.citation: Genome Res. 2013 Feb;23(2):377-87
references.pmid: 23064747
references.citation: Bioinformation. 2009 Apr 29;3(8):364-6
references.pmid: 19707302
references.citation: Bioinformatics. 2006 May 15;22(10):1177-82
references.pmid: 16446276
references.citation: J Mol Biol. 2000 Jul 28;300(5):1101-12
references.pmid: 10903857
references.citation: Nucleic Acids Res. 2008 Nov;36(20):6355-62
references.pmid: 18836192
references.citation: J Bioinform Comput Biol. 2004 Dec;2(4):681-98
references.pmid: 15617161
references.citation: PLoS Comput Biol. 2006 Apr;2(4):e33
references.pmid: 16628248
references.citation: RNA Biol. 2012 Jul;9(7):954-65
references.pmid: 22767260
references.citation: Algorithms Mol Biol. 2010 Dec 31;5:39
references.pmid: 21194463
references.citation: Mol Cell. 2011 Sep 16;43(6):880-91
references.pmid: 21925377
references.citation: PLoS Comput Biol. 2007 Apr 13;3(4):e65
references.pmid: 17432929
references.citation: RNA. 2011 Apr;17(4):578-94
references.pmid: 21357752
references.citation: BMC Bioinformatics. 2014 Mar 27;15:89
references.pmid: 24674136
references.citation: Nucleic Acids Res. 2006 Jan 10;34(1):53-65
references.pmid: 16407324
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2124-9
references.pmid: 21245330
references.citation: Genome Biol. 2007;8(4):R61
references.pmid: 17442114
references.citation: BMC Bioinformatics. 2013 Jun 07;14:184
references.pmid: 23758764
references.citation: Bioinformatics. 2008 Dec 15;24(24):2849-56
references.pmid: 18940824
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W373-7
references.pmid: 20444875
references.citation: Nat Biotechnol. 2009 May;27(5):455-7
references.pmid: 19430453
references.citation: Algorithms Mol Biol. 2010 Jan 04;5:5
references.pmid: 20047661
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W109-13
references.pmid: 18477632
references.citation: Genome Res. 2010 Jan;20(1):133-41
references.pmid: 19884261
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102
references.pmid: 19109441
references.citation: Bioinformatics. 2011 Feb 15;27(4):456-63
references.pmid: 21134894
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32
references.pmid: 23125362
references.citation: Nucleic Acids Res. 2006 May 22;34(9):2791-802
references.pmid: 16717284
references.citation: J Mol Biol. 1981 Mar 25;147(1):195-7
references.pmid: 7265238
references.citation: BMC Bioinformatics. 2008 Nov 11;9:474
references.pmid: 19014431
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21878-82
references.pmid: 19996181
references.citation: Arch Microbiol. 2010 Sep;192(9):691-702
references.pmid: 20559624
references.citation: PLoS Pathog. 2010 Mar 12;6(3):e1000809
references.pmid: 20300607
references.citation: Bioinformatics. 2008 Nov 15;24(22):2657-63
references.pmid: 18434344
references.citation: RNA Biol. 2010 Mar-Apr;7(2):120-4
references.pmid: 20220307
references.citation: Algorithms Mol Biol. 2010 May 21;5:22
references.pmid: 20492641
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9
references.pmid: 15665081
references.citation: Nucleic Acids Res. 2003 Apr 15;31(8):2187-95
references.pmid: 12682369
references.citation: Mol Microbiol. 2011 May;80(4):868-85
references.pmid: 21375594
references.citation: PLoS Comput Biol. 2008 Nov;4(11):e1000176
references.pmid: 19043537
references.citation: PLoS One. 2012;7(10):e45160
references.pmid: 23091593
references.citation: Proc Biol Sci. 1994 Mar 22;255(1344):279-84
references.pmid: 7517565
references.citation: RNA Biol. 2010 Jan-Feb;7(1):33-42
references.pmid: 20061798
references.citation: Algorithms Mol Biol. 2006 Mar 16;1(1):3
references.pmid: 16722605
references.citation: RNA Biol. 2013 Jul;10(7):1204-10
references.pmid: 23702463
references.citation: J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25
references.pmid: 17171697
references.citation: F1000 Biol Rep. 2010 Jan 27;2:8
references.pmid: 20495679
references.citation: Nature. 2010 Sep 2;467(7311):103-7
references.pmid: 20811459
references.citation: Nucleic Acids Res. 2012 Dec;40(22):11659-72
references.pmid: 23034808
references.citation: PLoS One. 2011;6(7):e22705
references.pmid: 21799937
references.citation: Curr Biol. 2001 Sep 4;11(17):1369-73
references.pmid: 11553332
references.citation: PLoS One. 2008 Sep 12;3(9):e3197
references.pmid: 18787707
references.citation: Genome Res. 2011 Sep;21(9):1487-97
references.pmid: 21665928
references.citation: Biochem Biophys Res Commun. 2008 Jul 25;372(2):346-50
references.pmid: 18501192
references.citation: Biochimie. 2002 Sep;84(9):925-44
references.pmid: 12458085
references.citation: Genes Dev. 2010 Dec 1;24(23):2621-6
references.pmid: 21123649
references.citation: J Mol Biol. 2002 Jun 21;319(5):1059-66
references.pmid: 12079347
references.citation: Nature. 2009 May 14;459(7244):266-9
references.pmid: 19444216
references.citation: Bioinformatics. 2010 Jan 1;26(1):1-5
references.pmid: 19850757
references.citation: PLoS Genet. 2013 May;9(5):e1003495
references.pmid: 23696746
references.citation: PLoS Comput Biol. 2009 Sep;5(9):e1000502
references.pmid: 19750212
references.citation: Algorithms Mol Biol. 2013 Apr 20;8:14
references.pmid: 23601347
references.citation: Bioinformatics. 2013 Nov 15;29(22):2933-5
references.pmid: 24008419
references.citation: RNA. 2012 May;18(5):900-14
references.pmid: 22450757
references.citation: Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96
references.pmid: 23980183
references.citation: BMC Genomics. 2011 Apr 27;12:207
references.pmid: 21524285
references.citation: Biochimie. 2011 Nov;93(11):2019-23
references.pmid: 21835221
references.citation: Mol Microbiol. 2011 Sep;81(5):1144-65
references.pmid: 21696468