Bio-informatic

Bio-informatic Fun

Facepalm Thursdays…

I was trying to build a Cazy reference database to explore the carbohydrate profiles of the genomes in our microbial laboratory collection. I have a parallel script downloading the proteins sequences from NCBI then aligning and creating a hmm profile for later use. This morning I am looking through the…

AdrienFebruary 17, 2022

Bio-informatic [PwD] H. pylori

[Playing with Data] 607 pylori part III: Start digging

Hello Folks, it's been a while! I thought it would be time to continue this big Helicobacter pylori genomes experiment and keep the blog going on. We left with the previous post on preparing the data for our analyses. The main next step will be re-annotating all the genomes in…

AdrienNovember 14, 2017

Bio-informatic [PwD] H. pylori

[Playing with Data] 607 pylori part II: getting the data ready

In the previous post we had a look at some interesting features of Helicobacter pylori. Now it is time to finally get our hands on the data. This post will present the data preparation, how to get everything ready in a comparable way for easy analyses.Now that we know more…

AdrienApril 17, 2017

Bio-informatic [PwD] H. pylori

[Playing with data] 607 pylori part I : the introduction

Every story or study needs an introduction to give some context to what we are look at. When I first started writing the introduction about Helicobacter pylori, I realised quite quickly that my first attempts were massively paraphrasing again and again Wikipedia's summary. Because the Wikipedia article contains most of…

AdrienApril 10, 2017

Bio-informatic [PwD] H. pylori

[Playing with Data] Comparing Helicobacter pylori genomes

With the upcoming gloom of an eventual unemployment period, I decided to fill my non existent free time with a fun little project I've has in mind for a while; as one of my previous post might have indicated. It is time to tackle it! I have been working with…

AdrienMarch 5, 2017

Bio-informatic Play with Data

[Playing with Data] Looking at a Fish pathogen genome

In this blog note I will use some of the techniques I used in my previous post to look at a recently published dataset. Last year I came across a study by the Institute for Veterinary Pathology, in Zürich, Switzerland describing a bacterial pathogen of fish. Aquaculture is a big…

AdrienSeptember 5, 2016

Bio-informatic

Fetching information from NCBI directly from the command line

I recently (re)discovered the edirect software package published on NCBI. As described on the website this "software suite that enables users to use the UNIX command line to directly access NCBI databases, as well as to parse and format the data to create customized downloads". How does it work? Basically…

AdrienJuly 26, 2016

Bio-informatic [PwD] H. pylori

[Playing with Data] A network of Pylori

So I am playing with the idea of genome comparison and network analysis. And as a small teaser I want to share the above picture. On this figure each dot represent a gene from one of the 83 more or less complete Helicobacter pylori genomes used in the comparison, linked…

AdrienJuly 5, 2016

Bio-informatic

Link dump – Fancy distinct colors

Writing the blog and the thesis at the same time appeared to be harder than expected. I will be back here soon enough ! In the mean time, I was looking to beautify R generated graphs and most of the time I got stuck in having to choose nice but…

AdrienMarch 9, 2016

Bio-informatic

Metagenome part 3: Binning the reads – the easy part

In the previous article we assembled a first version of the metagenome, using a fast assembler creating a lot of rather small contigs. We need now to separate these reads according to the different genomes present in the assembly: this is called binning. To tease apart the different genomes we…

AdrienJanuary 7, 2016

Interesting Publication