Tag Archives: microbial


Friday SNPpets

This week’s SNPpets include quite a range of things. New species genomes projects (pineapple is out, bauhinia being crowdfunded). I dare you to resist a tool called “Time Curves“.  The pre-print on over 60k protein coding human variations. Updates via FlyBase and discussed for QIIME. Best quip of the week: You can buy a DNA test on Amazon and it costs less than the textbook about it. A couple of items on bioinformatics pain. Some new solutions. And more….

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


Video Tip of the Week: e-PathGen, Using Genomics to Support Public Health

Recently I saw the Director of Public Health Genomics for the CDC tweet about a resource that was new to me, ePathGenPathogen Genomics for Epidemiology. This is an area that I’m glad to see getting attention. My undergrad degree was in microbiology, and certainly the most memorable class I had in college was about pathogenic bacteria and viruses and their consequences throughout history and to the present. One thing that was stressed to us, though, was that we could only study the things we could culture. Some things were really challenging to grow or couldn’t be grown at all with current methods. I was struck by this again in a seminar I heard where a physician described the assessment of the the organisms in a brain abscess sample, they were able to culture 22 organisms. With PCR, the same sample showed 72. Eek.

But our new abilities to look at unculturable organisms by sequencing them rapidly, and then to more quickly and appropriately target infections, is also even getting NYT press coverage at this point: In a First, Test of DNA Finds Root of Illness. And that’s just one kid’s illness–this can also be used to more quickly put the brakes on community-wide issues too. So here’s the tweet that caught my eye:

And I went to see what e-PathGen was about. What they provide are a couple of video tutorials–but I can’t embed them here, they are part of a learning module that also has additional details and two case studies to work through.  The tutorials offer some guidance for folks who might be new to genomics and the sequencing technology from a public health perspective. Then the two case studies show how this type of information might be used on a specific outbreak of illness.

So here’s a look at their landing page, and you can click to go over there and watch their videos:

ePathGen Tutorials and Case Studies -- click to visit them.

ePathGen Tutorials and Case Studies — click to visit them.

Or go to the site with this link: http://public-health-genomics.phe.org.uk/

And usually we like to highlight specific database resources or other bioinformatics tools in our tips. And in the first case study I came across a database collection that was new to me–the BIGSdb system, Bacterial Isolate Genome Sequence Database. This is a framework that offers researchers and clinicians a place to store details of specific isolates of patient or environmental samples. It doesn’t require whole genome data–but it is flexible enough to support that as well as we will increasingly see more of that kind of data coming along.

This framework has now been used by a number of different groups to create databases with their organisms of interest. Check out this list of organisms that you can find individual samples from: http://pubmlst.org/databases/. I hope to take a look at this in a future tip–I’ve already gone longer than I like to in our weekly introduction to a new resource. So check back with us for more on this later.

Quick links:

ePathGen videos and case studies: http://public-health-genomics.phe.org.uk/

Bacterial Isolate Genome Sequence Database (BIGSdb): http://pubmlst.org/software/database/bigsdb/

PubMLST: http://pubmlst.org/


Jefferies J. & McCulloch J. (2014). ePathGen – a new e-learning package in pathogen genomics., Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin, PMID:

Jolley K.A. & Maiden M.C.J. (2010). BIGSdb: Scalable analysis of bacterial genome variation at the population level., BMC bioinformatics, DOI:

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):


July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.


August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.


September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.


October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life


November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.


December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: Comparing Microbial Databases

A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I’ve been exploring & thinking since then & am going to give a very brief comparison of those two resources in today’s tip & I’ll expand the comparison to other resources here in the text of this post.

Continue reading

IMG extends capabilities

DOE JGI extended and updated the content of IMG and IMG/M recently as this linked press release shows (here is another), so today I’d like to just make a quick post to highlight that OpenHelix has a tutorial on IMG/M that is sponsored by JGI and thus free.

Metagenomics is a huge new field and IMG/M has some excellent tools and data!


Just a short post with some information:

Metagenomics is the new genomics :). NIH Roadmap has a new initiative, the Human Microbiome Project with a bit of funding :) . Meanwhile, other projects and databases are developing such as Integrated Microbial Genomes w/ Microbiome Samples (or IMG/M) and Camera. It’s an exciting and fascinating field (my former colleagues at the Bork lab just published interesting research in this field), though some scientists of course have their doubts.