Comments for michael barton

Comment on Discovering a plasmid in our sequence data by Michael Barton

Michael Barton — Tue, 16 Mar 2010 19:49:15 +0000

I've added an update the post – it's good to get feedback and discussion.

Comment on Discovering a plasmid in our sequence data by Michael Barton

Michael Barton — Tue, 16 Mar 2010 19:41:33 +0000

Thanks Morgan. You're right we won't know which is the case until we can either circularise the scaffold to produce a complete plasmid or bridge the gaps with the other scaffolds and integrate it into the genome build. We're planning to do this soon but at the moment though we're planning on crossing the smaller internal scaffold gaps.

Comment on Discovering a plasmid in our sequence data by Morgan Langille

Morgan Langille — Tue, 16 Mar 2010 07:14:26 +0000

I'm not really sure if your analysis confirms that it is a plamid. It could just as easily be a newly inserted region (maybe with a plamid intermediate) into the genome. Many of these large HGT events (or genomic islands (GIs)) will have these low sequence similarity scores. Pseudomonas is also well known for containing GIs.Good luck with your analysis!

Comment on Estimating genome scaffold order using reference genomes by Discovering a plasmid in our sequence data | michael barton

Discovering a plasmid in our sequence data | michael barton — Mon, 15 Mar 2010 09:06:41 +0000

[...] week I determined the likely order of our Pseudomonas fluorescens R124 sequencing scaffolds by mapping them on to reference genomes from the same species. This mapping to reference genomes also indicated two of the sequence scaffolds ( 5 and 8 ) [...]

Comment on First look at Pseudomonas fluorescens sequencing results by Estimating genome scaffold order using reference genomes | michael barton

Estimating genome scaffold order using reference genomes | michael barton — Mon, 08 Mar 2010 10:12:38 +0000

[...] P. fluorescens genome sequencing results arrived last week and so far I’ve been looking at how we can begin to assemble the scaffolds from the smaller [...]

Comment on First look at Pseudomonas fluorescens sequencing results by Michael Barton

Michael Barton — Tue, 02 Mar 2010 18:42:18 +0000

That's a good idea. I hadn't thought of that. I will try this.

Comment on First look at Pseudomonas fluorescens sequencing results by maximilianh

maximilianh — Tue, 02 Mar 2010 10:42:22 +0000

How much contamination did you find? Is there really no human genome contamination in there or any other bacteria? This is very simple to check: Just blast the human and some bacterial genomes (e.g. from NCBI's collection or ensemblGenomes) onto your sequences

Comment on Adapting to generating my own data by maximilianh

maximilianh — Tue, 16 Feb 2010 10:35:23 +0000

Welcome to biology!

Comment on Adapting to generating my own data by A combined approach to genome sequencing | michael barton

A combined approach to genome sequencing | michael barton — Mon, 15 Feb 2010 09:37:39 +0000

[...] but this was ruled out by the low coverage per genome (~9X) and additional sample preparation costs which I’ve discussed previously. So instead we’ll sequence two genomes on a 454 plate split in half using the standard rubber [...]

Comment on In yeast, the codon adaptation index explains variation in transcript levels but little in protein levels by My Domain

My Domain — Fri, 05 Feb 2010 01:22:07 +0000

Joe…

Check out my domain sometime….