Monthly Archives: December 2010

The reference to number of phages on Earth

I have always taken (and used) for granted the 1031 number of phages in the planet. Normally, this is calculated from the estimation that there are 10 phages per prokaryotic cells, and the latter are estimated to be 1030. Usually the references to these numbers are: Jiang & Paul 1998, PMID 9687430 and Whitman 1998, PMID 9618454

Today I found what might be an older reference: Bergh et al. 1989, PMID 2755508, High abundance of viruses found in aquatic environments

Once I get access to the full-text paper (“thanks to” Nature’s unwillingness to open even older articles), I can confirm the exact phage number as claimed in 1989.

If you know of a better (aka older) reference, feel free to share it.

This number (1031), by the way, can be read as: ten nonillions (by the US numbering system)

Using the SEED Servers

 

The Seed Servers are a newer way of accessing the SEED, but at the moment they are limited to the Argonne SEED. Rather than the SOAP based approach which is designed around a single call, the SEED servers are designed around sending larger chunks of data. If you are interested in using the SEED servers I have included a short demo in the read more.

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Accessing the SDSU Seed

The SDSU Seed (aka Phantome Seed, phage seed) is a complete local seed install. I mainly update the phages on this (because it is the phage seed), but can update microbial genomes if you need. If you want a more up to date site with microbial genomes check out the SEED servers (and my separate blog post about using those).

In the read more I detail how to access the local SEED if you are interested.

 

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Annotate Metagenomes In An Instant

RTMg has been available a while, and we have done some pretty cool stuff with it [e.g. web, mobile, open social, and all publicly available metagenomes], but we need to enable others to play with it too. Now everyone can enjoy metagenome annotation in an instant. (Not the flavorless instant coffee type instant, but the rich and bountiful instant gratification type instant!). Don’t believe me? Here is a video I made showing how to annotate a metagenome and create a pie chart of the data.

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After the read more I’ll show you how to do it too.

 

 

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