Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences

BMC Bioinformatics

Volumn 4, Issue , 2003, Pages

  Purohit, H J ^a   Raje, D V ^a   Kapley, A ^a  

^a NATIONAL ENVIRONMENTAL ENGINEERING RESEARCH INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA 16S; NUCLEOTIDE; PRIMER DNA; HETERODUPLEX; RIBOSOME DNA; RNA 16S;

ANIMAL CELL; ARTICLE; BACTERIAL GENETICS; BACTERIAL SURVIVAL; BASE MISPAIRING; COMPUTER PROGRAM; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; ENTROPY; GENE DELETION; GENE INSERTION; GENE LOCATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENUS; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SEQUENCE ALIGNMENT; SOIL MICROFLORA; SPECIES DIFFERENCE; SPECIES HABITAT; GENETICS; HETERODUPLEX ANALYSIS; METHODOLOGY;

BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; PSEUDOMONAS;

BASE PAIR MISMATCH; CONSERVED SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; HETERODUPLEX ANALYSIS; NUCLEIC ACID HETERODUPLEXES; POLYMERASE CHAIN REACTION; PSEUDOMONAS; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 0141988247     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-19     Document Type: Article

References (22)

1. Atuanya EI, Purohit HJ and Chakrabarti T Anaerobic and aerobic biodegradation ofchlorophenols using UASB and ASG bioreactors World Journal of Microbiology & Biotechnology 2000, 16:95-98
2. Chhatre SA, Purohit HJ, Shanker R, Chakrabarti T and Khanna P Bacterial consortia for crude oil spill remediation Water Science and Technology 1996, 34:187-193
3. Kapley A, Purohit HJ, Chhatre S, Shanker R, Chakrabarti T and Khanna P Osmotolerance and hydrocarbon degradation by genetically engineered bacterial consortium Bio-Resource Technology 1999, 67:241-245
4. Kapley A, Lampel K and Purohit HJ Thermocycling steps and optimization of multiplex PCR Biotechnology Letters 2000, 22:1913-1918
5. Kapley A and Purohit HJ Tracking of phenol degrading genotype Environmental Science and Pollution Research 2001, 8:89-90
6. Kutty R, Purohit HJ and Khanna P Isolation and Characterization of a Pseudomonas sp. strain PH1 utilizing meta-aminophenol Canadian Journal of Microbiology 2000, 46:211-217
7. Lowe T, Sherfkin J, Yang SQ and Dieffenbach CW A computer program for selection of oligonucleotide primers for polymerase chain reaction Nucleic Acids Research 1990, 18:1757-1761
8. Mitsuhashi M, Cooper A, Ogura M, Shinagawa T, Yano K and Hosokawa T Oligonucleotide probe design - a new approach Nature 1994, 367:759-761
9. Feng DF and Doolittle RF Progressive sequence alignment as a prerequisite to correct phylogenetic trees Journal of Molecular Evolution 1987, 25:351-360
10. Lipman DJ, Altschul SF and Kececioglu JD A tool for multiple sequence alignment Proceedings of National Academy of Science 1989, 86:4412-4415
11. Thompson JD, Higgins DG and Gibson TJ CulstalW: improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 1994, 22:4673-4680
12. Thompson JD, Plewniak F and Poch O A comprehensive comparison of multiple sequence alignment programs Nucleic Acids Research 1999, 27:2682-2690
13. Hyndman D, Cooper A, Pruzinsky S, Coad D and Mitsuhashi M Software to determine optimal oligonucleotide sequences based on hybridization simulation data BioTechniques 1996, 20:1090-1096
14. Ashelford KE, Weightman AJ and Fry JC PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database Nucleic Acids Research 2002, 30(15):3481-3489
15. Raje DV, Purohit HJ and Singh RN Distinguishing features of 16S rDNA gene for five dominating bacterial genus observed in bioremediation Journal of Computational Biology 2002, 9(6):819-829
16. Fumigalli L, Taberlet P, Favre L and Hauser J Origin and evolution of homologous repeated sequences in mitochondrial DNA control region of shrews Molecular Biology and Evolution 1996, 13:31-46
17. Wilkinson GS, Mayer F, Kerth G and Petri B Evolution of repeated sequence arrays in evening bat D-loop mtDNA Genetics 1997, 128:607-617
18. Liu BH Statistical Genomics: Linkage, Mapping and QTL analysis CRC Press LLC, Florida 1998,
19. Rigoutsos I and Floratos A Combinatorial Pattern Discovery in Biological Sequences: the TEIRESIAS Algorithm Bioinformatics 1998, 14:55-67
20. Kurtz S and Schleiermacher C REPuter: fast computation of maximal repeats in complete genomes Bioinformatics 1999, 15:426-427
21. Kurtz S, Choudhari J, Schleiermacher C, Stoye J and Giegerich R REPuter: the manifold applications of repeat analysis on a genome scale Nucleic Acids Research 2001, 29:4633-4642
22. Durbin R, Eddy S, Krough A and Mitchison G Biological Sequence Analysis: Probabilistic models for proteins and nucleic acids Cambridge University Press 1998.