Comments for michael barton

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….

Comment on Genomics in a small microbiology lab by Michael Barton

Michael Barton — Wed, 13 Jan 2010 21:12:26 +0000

Hi Neil.

Things are quite hard at the moment. I'm trying to learn as much as possible about genome sequencing and assembly while as the same time reading about microbial genomics and diversity. I'm spending most of my time reading really. I'm realising genomics and genome assembly is a massive field.

We've been developing a few research questions. I've been updating a wiki for the project as I've been going along (http://bit.ly/8ysBG0). In short there are a couple of P. fluorescens strains that have been sequenced from plants so we're going to see if the strains in caves show markedly different metabolism and genome variability.

I've heard you've been having quite a lot of snow in Manchester.

Comment on Genomics in a small microbiology lab by Neil Swainston

Neil Swainston — Wed, 13 Jan 2010 13:06:30 +0000

Hi Michael, how's it going?

Any further ideas regarding your research question? What is your interest in these microorganisms?

Cheers,

Neil.

Comment on Genomics in a small microbiology lab by Neil Swainston

Neil Swainston — Wed, 13 Jan 2010 08:06:30 +0000

Hi Michael, how's it going?

Any further ideas regarding your research question? What is your interest in these microorganisms?

Cheers,

Neil.

Comment on Deciding what genomes to sequence by michaelbarton

michaelbarton — Mon, 11 Jan 2010 18:49:13 +0000

Hi Pedro,

Thanks for your comment. It's nice to receive feedback on my ideas now that I'm the only bioinformatician in my department. I'd like to do the second between cave analysis but I worry that we won't have enough sequence data from 454 for four genomes. The P. fluorescens genomes are quite large so it's possible that we won't get enough coverage. I guess we don't need a complete assembly of the genome just enough to find most of the gene complete in each isolate.