IWoCS: Analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships

Bioinformatics

Volumn 22, Issue 5, 2006, Pages 527-531

  D'Auria, Giuseppe ^a   Pushker, Ravindra ^a   Rodriguez Valera, Francisco ^a  

^a MIGUEL HERNÁNDEZ UNIVERSITY   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOMAL SPACER DNA; TRANSFER RNA;

ARTICLE; BACTERIUM IDENTIFICATION; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENETIC CONSERVATION; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; TAXONOMY;

BACTERIA (MICROORGANISMS);

EID: 33644856111     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btk033     Document Type: Article

References (21)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Baudart,J. et al. (2000) Diversity of Salmonella strains isolated from the aquatic environment as determined by serotyping and amplification of the ribosomal DNA spacer regions. Appl. Environ. Microbiol., 66, 1544-1552.
3. Boyer,S.L. et al. (2001) Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria. Mol. Biol. Evol., 18, 1057-1069.
4. Chang,H.C. et al. (2005) Species-level identification of isolates of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex by sequence analysis of the 16S-23S rRNA gene spacer region. J. Clin. Microbiol., 43, 1632-1639.
5. Clementino,M.M. et al. (2001) PCR analyses of tRNA intergenic spacer, 16S-23S internal transcribed spacer, and randomly amplified polymorphic DNA reveal inter- and intraspecific relationships of Enterobacter cloacae strains. J. Clin. Microbiol., 39, 3865-3870.
6. Daffonchio,D. et al. (2003) Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera. Appl. Environ. Microbiol., 69, 5128-5137.
7. Deschavanne,P.J. et al. (1999) Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol., 16, 1391-1399.
8. Fadiel,A. et al. (2003) Remarkable sequence signatures in archaeal genomes. Archaea, 1, 185-190.
9. Garcia-Martinez,J. and Rodriguez-Valera,F. (2000) Microdiversity of uncultured marine prokaryotes: The SAR11 cluster and the marine Archaea of Group I. Mol. Ecol., 9, 935-948.
10. Garcia-Martinez,J. et al. (2001) RISSC: A novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Res., 29, 178-180.
11. Garcia-Martinez,J. et al. (2002) Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions. Environ. Microbiol., 4, 42-50.
12. Harper,D.A.T (1999) Numerical Palaeobiology. (ed). John Wiley and Sons, New York.
13. Iteman,I. et al. (2000) Comparison of conserved structural and regulatory domains within divergent 16S rRNA-23S rRNA spacer sequence of cyanobacteria. Microbiol., 146, 1275-1286.
14. 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.
15. Milyutina,I.A. et al. (2004) Intragenomic heterogeneity of the 16S rRNA-23S rRNA internal transcribed spacer among Pseudomonas syringae and Pseudomonas fluorescens strains. FEMS Microbiol. Lett., 239, 17-23.
16. Pushker,R. et al. (2005) Micro-Mar: A database for dynamic representation of marine microbial biodiversity. BMC Bioinformatics, 6, 222.
17. Rice,P. et al. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
18. Rocap,G. et al. (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl. Environ. Microbiol., 68, 1180-1191.
19. Suzuki,M.T. et al. (2001) Phylogenetical analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ. Microbiol., 3, 323-331.
20. Teeling,H. et al. (2004) TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 5, 163.
21. Wang,Y. et al. (2005) The spectrum of genomic signatures: From dinucleotides to chaos game representation. Gene, 346, 173-185.