Tag Archives: virus

Tip of the Week: VirusMINT

virusMINTThe MINT or Molecular Interaction database for examination of protein interaction networks has long been a favorite tool of mine.   The regular “flavor” of MINT includes over 100,000 interactions with a focus on experimentally verified protein interaction data.  But recently I became aware of the VirusMINT data that is now available as well.

The VirusMINT paper describes the initial emphasis on medically relevant viruses for their curation efforts, and how the work differs from efforts like this PLoS Pathogens paper and the individual virus sites like NCBI’s HIV Interactions collection and the PIG (Pathogen Interaction Gateway) site.

Manual curation of data is labor-intensive, but I really appreciate the quality of that data.  Some of the data they curated themselves, and some was downloaded from existing curated sites.  Once at the site for VirusMINT, it is really simple to load up a virus network by simply clicking on a virus button, and then the proteins load and generate a network interaction group.  The proteins are clickable and you can find out more about the proteins and their sources, and domain information if that is available.  You can also click on the numbers between the interactions to find out which paper provided the interaction data and link quickly to PubMed from there.  And not only can you interact with the data using the MINT software framework, but you can download the data and use it in other tools as well.

This brief Tip-of-the-Week introduces a few of the basic features of VirusMINT.  We have additional details about how to interact with the software in our full MINT tutorial.

Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., Cusick, M., & Cesareni, G. (2009). VirusMINT: a viral protein interaction database Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn739

VirusMINT site directly: http://mint.bio.uniroma2.it/virusmint/Welcome.do

MINT main site directly: http://mint.bio.uniroma2.it/mint/Welcome.do

Tip of the Week: ViralZone at ExPASy

viralzone_tip For today’s tip I am going to continue with the theme I started yesterday – obtaining swine flu information. There are many wonderful viral resources that are publicly available. I  linked to NCBI’s Influenza Virus Resource in yesterdays post, and you can watch past tips that Trey has done tips on the Viral Bioinformatics Resource Center (VBRC) here and here. But for todays tip I’ve like to introduce you to the ViralZone, which is available from the ExPASy Proteomics Server.  ViralZone is  created by the Swiss Institute of Bioinformatics (SIB) and provides a really clear, concise introduction to a virus as well as links to any variety of detailed information.

Swine Flu: What's the Populous to Do?

Well, as far as I can tell, read & do all the normal stuff for staying healthy (you know, all the stuff Mom used to say – wash your hands, drink plenty of liquids, eat right & get plenty of sleep.) I heard about swine flu as I woke up yesterday morning listening to NPR, and the coverage of the “outbreak” seems to be spreading more virally than the virus itself. PubMed already has a special section of their homepage dedicated to swine flu info, with links to recent PubMed articles,  a link to the swine flu sequence in NCBI’s Influenza Virus Resource, and a widget to CDC’s swine flu information page.  Through one of the PubMed references I found a resource I had not heard of before – ESNIP2 – the European Surveillance Network for Influenza in Pigs.  From the sequence report I could like to structures in NCBIsmall_world_3‘s MMDB and from there to structures in RCSB PDB.  From the CDC’s site I followed a link to an update from the World Health Organization which reported the number of cases and deaths in various world locations. I find it really cool to be able to link so freely between biological/health information resources, and be able to counter all the popular media frenzy with reports of real science. And the fear mongering seems to be just that, at least for now, because nothing that I’ve read so far indicates that swine flu is any more deadly or virulent than ‘normal’ seasonal flu – it is just a different virus than we normally see.

Yea, ok, we live in a small world where people move around and potentially spread diseases far and wide. But there is so much information at our finger tips – with an internet connection and a bit of knowledge where to look. I’ll continue to take my risks, travel, read science, and of course listen to Mom & wash my hands! :)

Addition (Trey): These are some great resources that Jennifer linked to. I’d like to include some additional general and genomic data too. I’ll add more as I find them:

Kristi at Bioinformatics@Becker (she’s here at Wash U where we are giving a seminar today) has a great post with links to many general and science links.

BioHealthBase has the swine flu strain genome details. BioHealthBase “provides a comprehensive genomic and proteomic data repository for five pathogenic organism groups that pose a threat to public health”

Effect Measure is a MUST read blog for anything public health policy and science related, and is a great read right now.

A short primer on the science of the swine flu.

Cold genomes

coldvirusRecently, we are learning a lot about the cold virus. The genomes of many have now been sequenced (that is a subscription-required Science report, you can read more about the report here).

You can find more genomic information at the picornaviridae.com at the NCBI’s Entrez Genomes and some structural information at MMDB. (just a side note, rhinovirus is now classified as enterovirus).

Tip of the Week: A quick annotation of a genome

gatu tip thumbnailHey, say you’ve got a bacterial genome you just sequenced in your spare time (hey, the way technology is going, it’s not far off) and you need to do a quick and dirty annotation to get you started. Well, there are several tools out there to do that, predict genes, annotate regions, etc. I’d like to show you one in this tip that you might not have thought of but could be a useful tool to get started. It’s GATU (Genome Annotation Transfer Utility) at VBRC. As the name suggests, this doesn’t do any major gene predicting, what it does is take your genome and compare it to a closely related genome (the closer the better of course) and transfers all the annotation from the characterized genome. This is from a viral resource (VBRC) but it works just as well with bacterial genomes, something that might not have been obvious and puts another tool in your belt.