Bacterial 16S, 23S molecular identification

With the rapid development of
molecular biology
, the classification of bacteria has also goes from traditional esoteric classification to various
-gene
classification levels, such as (G-C) mo l,
DNA
hybridization, rDNA fingerprinting, mass particle spectrometography, and 16S rDNA sequence analysis.
rRNA is present in all bacteria, and the rRNA gene consists of conservative and variable regions, which are highly conservative in bacteria. The rRNA gene contains several components from 5' end to 3' end, namely 16S rDNA, inter-region, 23S rDNA, inter-region, and 5S rDNA. Due to the highly conservative nature of the 16S rDNA sequence in prokerative organisms, the identification of similar species or different strains within the same species is poor. 23S rRNA molecules are relatively large (about 3kb) and only a few
nucleic acid
sequences have been reported, which have not yet been widely used in the classification and identification of bacteria.
16S-23S rDNA inter-region (Intergenic Spacer Region, ISR) has been the focus of much attention in recent years for bacterial identification and classification due to the lack of specific functions and the evolutionary rate of more than 10 times greater than 16S rDNA. The number, size and sequence of 16S223S rDNA ISRs of some bacteria have been reported, and the differences between them give them a place in the development of bacterial systems, especially in the differentiation and identification of similar species and strains.
PCR
-RFLP
through PCR amplification of a piece of DNA on mycobacteria chromosomes, the amplification of the product is digested by restrictive endoenzymes, the digested samples are
agargic
glycogel electrophoresis analysis, different mycobacterial enzymes
slices
segments of the number or size of different, electrophoretic map spectrum is multi-state.
Such as 16-23srDNA gene PCR amplification, amplification fragment (350bp) after the identification of 4 base sequences of the restrictive endoenzyme Hae III. MPPI enzyme after digestion analysis, can identify different mycobacteria complex. For PCR amplification of 16sr DNA fragments specific to mycobacteria genus, the resulting DNA fragments (1500bp) are digested by CfoI, MboI, RsaI enzymes, and the electrophoretic analysis enzyme spectrometography can also be identified for Mycobacteria.
thermal shock protein (hsp65) gene conservative, present in all mycobacteria, with PCR amplification of hsp65 a piece of gene fragments (439bp) and with BstEII. and HeaII. enzyme digestion analysis of 34 kinds of mycobacteria, showing different molecular weights of the band map.
Plikayti amplified the specimen hsp65 gene, resulting in a sequence of 1380bp, digestive amplification with BstEII. and XhoI, 19 common mycobacteria produced a identifiable band type, the method can identify more than 90% of pathogenic Mycobacteria. In addition, Niemann amplified a fragment of 1020bp to the gyrB DNA sequence, using three restrictive enzymes to separate the mycobacteria tuberculosis complex. The key to USPCR-RFLP is the design of the quotation and the choice of the endoenzyme.
related software
phylip 3.6a3 Evolutionary Tree Analysis software and can map EvolutionAry Tree
TreeView 1.6.6 Evolutionary Tree Processing Software
GeneTree 1.6 3 Programs for Comparing Genes and Species Evolutionary Trees
NDE 0.5.0 Programs for Editing NEXUS Format Files
TreeMap 1.0 Programs for Visually Comparing The Master from Evolutionary Tree

Spectrum analyzes evolutionary information without turning it into evolutionary tree software
Phyltools 1.32 Software for calculating and processing evolutionary tree data
tree-puzzle 5.0 nucleic acid sequences, protein sequence similarity analysis, and evolutionary tree building tools
ATV 1.92 JAVA language displays "New Hampshire" and NHX format evolutionary tree file software
TREECON 1.3 Software packages for building and mapping evolutionary trees
ProBiosys 1.0 Software for comparative express taxonome data and analysis to calculate nucleic acid sequence data distance values
COMPONENT 2.0 Analysis Evolutionary Tree Free software
NJplot's compact display evolutionary tree for free software NJplot
MEGA 2.1 Free Molecular Evolution Genetic Analysis Software
UP 4 4 PAUP's Quick Use Manual
Bacteria If this refers to a narrow primary nucleus
microbials
identification can only be analyzed with 16SrDNA sequence, because 23SrDNA is unique to the uterior organism, so if the bacteria here refer to a broad microorganism, you first have to work into two pieces, one primary nucleus with 16SrDNA, the other with 23SrDNA.
as for the writing of the software personal think DNA star is better, foreign researchers also have a lot of use of this software, generally recognized this software, the function is also relatively complete.