Bacterial Genome Comparison

Giorgio C · 11-03-2012, 10:31 PM

Hi all,

After a metagenome 16S microbiome project, we have been interested to whole sequence a bacteria genome of our interest in 3 different subjects.
Now I have 3 whole genomes of the same bacteria (belong to 3 different subjects) and I would like to compare those with the public annoted genome of the same bacteria. The sequences have been obtained on a 454 run. What tool do you suggest to use, what type of workflow?

On my experience, I would first try an assebly with gsAssembler and than a mapping with the gsMapper, but I don't know if it's the correct way and above all after that I don't know how to handle the large amount of data generated (for example I am interested in looking for changes in crucial genes that may cause a switch bethween a pathogen version of the bacteria).

I hope you have any idea on how proceed. Any input it's higly appreciated.

Thanks in advance,
Giorgio

Jo84 · 11-04-2012, 01:13 AM

Hi Giorgio,
I'm Giorgia and I'm a PhD student in microbiology.
I'm supposed to 16S rDNA sequencing to identify the community in soil samples treated with pesticides.
My problem is: 16S rDNA sequencing with Illumina (through Mate Pair sequencing) or 454?
I would need your own opinion.
Thank you
Giorgia

Giorgio C · 11-04-2012, 01:40 PM

Hi Giorgia,

wich type of illumina instrument do you have? How many different samples are you going to sequences? And just in general what's the question are you going to answer?

thanks,
Giorgio

Jo84 · 11-05-2012, 10:29 AM

I have to start my PhD. My project is identify the bacterial community of soil resistant to treatments with pesticides. My question was to know an opinion of other researchers using as a platform to sequence the 16S rDNA.
I'm a researcher with the first weapons.
Thanks
Giorgia

Giorgio C · 11-05-2012, 10:48 AM

Yes I see, as I told you before it depends...I personally sequenced in a 454flx+ 20 metagenome belong to 20 different subjects (both 16S and 18S) obtaining an avarage of 3000 high quality filtered sequences ready for the anaylis, that are enough to have a good taxonomic idea on what you are looking for. But in your case you did not tell me how many samples are u going to analyze. Anyway the last illumina instrumen seems to be better in terms of amount of sequences even if 454 gives you longer reads that are ideal for 16SrRNA (400-500 bp). You should considere different things depending on your exepriments and the cost you can afford; After that I absolutely reccomndand you a tool called 'Qiime' (www.qiime.org) for your analysis, it works great for 454 or illumina data as well.
Let me know if you need any help
Giorgio

Jo84 · 11-06-2012, 12:43 AM

Thanks for your help
Giorgia

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11-03-2012, 10:31 PM	#1
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Bacterial Genome Comparison Hi all, After a metagenome 16S microbiome project, we have been interested to whole sequence a bacteria genome of our interest in 3 different subjects. Now I have 3 whole genomes of the same bacteria (belong to 3 different subjects) and I would like to compare those with the public annoted genome of the same bacteria. The sequences have been obtained on a 454 run. What tool do you suggest to use, what type of workflow? On my experience, I would first try an assebly with gsAssembler and than a mapping with the gsMapper, but I don't know if it's the correct way and above all after that I don't know how to handle the large amount of data generated (for example I am interested in looking for changes in crucial genes that may cause a switch bethween a pathogen version of the bacteria). I hope you have any idea on how proceed. Any input it's higly appreciated. Thanks in advance, Giorgio

11-04-2012, 01:13 AM	#2
Jo84 Junior Member Location: Italy Join Date: Nov 2012 Posts: 5	Hi Giorgio, I'm Giorgia and I'm a PhD student in microbiology. I'm supposed to 16S rDNA sequencing to identify the community in soil samples treated with pesticides. My problem is: 16S rDNA sequencing with Illumina (through Mate Pair sequencing) or 454? I would need your own opinion. Thank you Giorgia

11-04-2012, 01:40 PM	#3
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Hi Giorgia, wich type of illumina instrument do you have? How many different samples are you going to sequences? And just in general what's the question are you going to answer? thanks, Giorgio

11-05-2012, 10:29 AM	#4
Jo84 Junior Member Location: Italy Join Date: Nov 2012 Posts: 5	I have to start my PhD. My project is identify the bacterial community of soil resistant to treatments with pesticides. My question was to know an opinion of other researchers using as a platform to sequence the 16S rDNA. I'm a researcher with the first weapons. Thanks Giorgia

11-05-2012, 10:48 AM	#5
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Yes I see, as I told you before it depends...I personally sequenced in a 454flx+ 20 metagenome belong to 20 different subjects (both 16S and 18S) obtaining an avarage of 3000 high quality filtered sequences ready for the anaylis, that are enough to have a good taxonomic idea on what you are looking for. But in your case you did not tell me how many samples are u going to analyze. Anyway the last illumina instrumen seems to be better in terms of amount of sequences even if 454 gives you longer reads that are ideal for 16SrRNA (400-500 bp). You should considere different things depending on your exepriments and the cost you can afford; After that I absolutely reccomndand you a tool called 'Qiime' (www.qiime.org) for your analysis, it works great for 454 or illumina data as well. Let me know if you need any help Giorgio

11-06-2012, 12:43 AM	#6
Jo84 Junior Member Location: Italy Join Date: Nov 2012 Posts: 5	Thanks for your help Giorgia