How to annotate a metagenome

First, you’ll need a fasta file. There is one here called 51.hits.fa that I like because pretty much every sequence will hit, and its reasonably small. And yes, it fits on the sd card 🙂 (it’s 1.2 M).

Go to this website:

There is a really vanilla upload form. It takes the following options:

a. ‘uploadedfile’ – this is the file name in a file input field.

b. ‘stringency’ – an integer between 1 and 4

c. ‘level’ – an integer between 0 and 5.

  • 0 : function
  • 1 : Subsystems
  • 2 : One level hierarchy
  • 3 : Two level hierarchy
  • 4 : Three level hierarchy
  • 5 : OTUs

At the moment only levels 0 and 5 work – the other levels return the same results as level 0. I’ll fix that soon.

Of course, if you know how to make a call with a file in a POST method, you don’t need to use this form!!

This will return a JSON formatted string like this:


There are two values, a URL and a max. In this case the max is 3. You need to call the URL with 1, 2, and 3 appended to the string to get the data for each fraction of the input file (ie. from 1 to max times).

Calling the URL will return another JSON formatted object that is basically a hash where the keys are the functions, subsystems, or OTUs, and the values are the number of occurrences. Each time you call it, sum up the numbers and display them somehow.