I have got a sequence for 16sr RNA gene of a bacterium. After constructing a phylogenetic tree by Mega 5 I am interested to further interpretation by using some other bioinformatic tools.
use the RDP classifier tool: rdp.cme.msu.edu/classifier/classifier.jsp
The range of software, used for phylogenetic recontructions are extremely wide today. And what software to use depend on particular goal of your research and some another condititons (i.e. operation system on your PC or somthing else).
Phylip, PAUP, Garli or another software also can be used for phylogenetic tree constructing. (Phylip and Garli are free) If you want to contruct secondary structure of this sequence, you can use Mfold and 4SALE.
But if you know what you want to obtain as a final result, I can to provide somthig more concrete information.
If you add some more detail of your data, we could try to better help you... For example which kind of research is it, taxonomical or of microbial community ecology? and ho many sequences you need to manage and analyze alltogheter?
Hi,
Have you tried Qiime? It's a really neat workflow for 16S analysis with great manuals and tutorials. There are several ways to install it ranging from source code, to a virtual machine that's already fully functional, to an instance on Amazon, so no time wasted on trying to get the software to work. See http://qiime.org/ for more info.
From your answer i deduce you have only one to several near full length 16S rRNA gene sequences?!
Insofar tools that cope with 16S community data are probably not those you're interested in., i.e. Mothur, QIIME, UPARSE. Those are very nice, complete, and helpful if you have amplified 16S data originating from a environmental community sequenced by some NGS technology (keyword: OTU-analysis), but if you have only a hand full of (probably Sanger sequenced near full length) 16S genes, than simple phylogenetic tree reconstruction is more or less the most and best you can do. For that i would highly recommend to use maximum likelihood approaches (like RAxML) as an alternative or at least as an addition to maximum parsimonious methods. PAUP and Phylip are, as far as i know, able to provide both approaches. But as already mentioned, there are many many tools in this field. So some more information about the nature of your data and on the hypothesis you're trying to resolve could yield more concrete tips.
Thanks Alessio and Andrii, But I have got the classification by blastN. Formation of tree by neighbour joining method have been done by Mega 5. How can I ellucidate important features of this 16s rRNA sequence by using bioinformative tools? Moreover I have got accession number of this gene on NCBI GENBANK.
how can we interpret various portions within this 16s rRNA gene sequence in context to the other deposited genes ?
or what can be the different in our strain with that of the mostly closest match by NCBI blastn?
Dear Ali,
i think so 16s rRNA is use only for identification of bacterial strain upto genus level so if you want to compare your bacterial genus with other then use maximum likelyhood by mega5 but if want to know specie then use housekeeping genes analysis. As regards to bioinformatic not much to to do only phylogenetics approaches because 16s rRNA gene not code any protein so not check expression, most of the bioinformatics work related to protein analysis of any gene.
hope it help you, stay blessed.
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