How to compare microbe genomic organisation?

Question: How to compare microbe genomic organisation?

4.1 years ago by

United States

How to search the genomic sequence of any microbe such as bacteria and then compare its genomic organisation with that of gene cluster present in putative enzyme of our use?

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Title moderated, original one:

How to get the genomic DNA structure of any microbe such as Streptomyces. natalensis ATCC 27448 and compare sequence similarity with genomic cluster of any enzyme present in it?

functional annotation alignment reference genomes • 816 views

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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by ankitanigam1211 • 0

4.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A great source for bacterial genome annotation is the UCSC Microbes Browser at http://microbes.ucsc.edu/

You will notice that many have comparative tracks based on similarity to known proteins already generated. You can also pursue a similar methodology yourself to perform cross-species annotation. What you eventually will want to do is map any annotation hits to a reference database that will provide EC numbers.

Once you have gene bounds/regions identified as targets, genome conservation "multiple-alignments" (the output often call "MAF" format) are where you'll want to go next. Not all genomes have this pre-computed nor will be in genome clusters that suite your research. And this can be a slightly tedious process to go through. Still, review how MAFs are created at UCSC in these track's methods, Microbes (link above) or others at http://genome.ucsc.edu. This particular method is the gold standard as far as I am concerned for global genomic arrangement analysis.

When you review methods, in the above or other publications (my short-hard here this is how much discovery/annotation is done, more or less, but look at pubs in your field), many tools to perform these operations will be in the Tool Shed http://usegalaxy.org/toolshed, as will alternate tools to perform similar functions, for most any data you wish to generate. Others tools can be wrapped and added. Test and build a workflow. These are for use in a local/cloud Galaxy: http://wiki.galaxyproject.org/BigPicture/Choices

Others who are currently performing bacterial analysis such as this are welcome to post more info (please!), Jen, Galaxy team

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