Bioinformatic discovery of bacterial regulatory RNAs using SIPHT

Methods in Molecular Biology

Volumn 905, Issue , 2012, Pages 3-14

  Livny, Jonathan ^a,b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Annotation; Bioinformatics; regRNA; SIPHT; sRNA

Indexed keywords

BACTERIAL RNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENE LOCUS; GENETICS; INTERNET; METHODOLOGY; MOLECULAR GENETICS; REGULATORY RNA SEQUENCE; REPLICON;

COMPUTATIONAL BIOLOGY; GENETIC LOCI; INTERNET; MOLECULAR SEQUENCE ANNOTATION; REGULATORY SEQUENCES, RIBONUCLEIC ACID; REPLICON; RNA, BACTERIAL; SOFTWARE;

BACTERIA (MICROORGANISMS);

EID: 84864128142     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-949-5_1     Document Type: Article

References (24)

1. Altuvia S (2007) Identi fi cation of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol 10:257-261
2. Sorek R, Cossart P (2010) Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9-16
3. Weissenmayer BA et al (2011) Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identi fi es seventy novel small non-coding RNAs. PLoS One 6:e17570
4. Liu JM et al (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37:e46
5. Livny J, Waldor MK (2010) Mining regulatory 5 ¢ UTRs from cDNA deep sequencing datasets. Nucleic Acids Res 38:1504-1514
6. Irnov I et al (2010) Identi fi cation of regulatory RNAs in Bacillus subtilis . Nucleic Acids Res 38:6637-6651
7. Sharma CM et al (2010) The primary transcriptome of the major human pathogen Helicobacter pylori . Nature 464:250-255
8. Mraheil MA et al (2011) The intracellular sRNA transcriptome of Listeria monocytogene s during growth in macrophages. Nucleic Acids Res 39:4235-4248
9. Livny J, Waldor MK (2007) Identi fi cation of small RNAs in diverse bacterial species. Curr Opin Microbiol 10:96-101
10. Lu X et al (2011) Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 17:1635-1647
11. Livny J et al (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 3:e3197
12. Valverde C et al (2008) Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 9:416
13. Faucher SP et al (2010) Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci USA 107:7533-7538
14. Dichiara JM et al (2010) Multiple small RNAs identi fi ed in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis . Nucleic Acids Res 38:4067-4078
15. Postic G et al (2010) Identi fi cation of small RNAs in Francisella tularensis . BMC Genomics 11:625
16. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
17. Macke TJ et al (2001) RNAMotif, an RNA secondary structure de fi nition and search algorithm. Nucleic Acids Res 29:4724-4735
18. Kingsford CL et al (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8:R22
19. Wassarman K et al (2001) Identi fi cation of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637-1651
20. Barrick JE, Breaker RR (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8:R239
21. Gardner PP et al (2011) Rfam: Wikipedia, clans and the decimal release. Nucleic Acids Res 39:D141-D145
22. Hulton CS et al (1991) ERIC sequences: A novel family of repetitive elements in the genomes of Escherichia coli , Salmonella typhimurium and other enterobacteria. Mol Microbiol 5:825-834
23. Rivas E et al (2001) Computational identi fi cation of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369-1373
24. van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31:3593-3596