Duncan Hull's blog has moved

If you're here looking for Duncan Hull's blog, it has moved to O'Really?. Nodalpoint lives on at nodalpoint.org.

Under MAFFT's hood


I am trying to learn what exactly MAFFT does to align sequences, but i am currently having a hard time to understand it.
I have read its papers and references.
Anyone knows of some kind of tutorial or review for it?

I am researching the FFT-NS-i and E-INS-i algorithms.

Currently, i am trying to understand what are the 6-tuples parameters. I guess the 6-tuples are the weight, volume and charge, compared in pairs of sequences. Is that right?

Thanks in advance

Just in case someone is interested:

Nodalpoint is now indexed by Google Scholar

Who's afraid of Google?Nodalpoint has been obviously indexed by Google for a long time now, but did you know it is also indexed and counted by Google Scholar too? See Mistaken Identity: Google thinks I'm Maurice Wilkins for details...

ANNOUNCE - Turnkey BLAST Servers on Amazon EC2

Cumulo Software has just released turnkey BLAST servers on EC2. The BLAST servers handle web service requests in a simple format. You can start as many servers as you need to achieve your desired throughput. It uses the latest BLAST+ software and databases. More information is located at http://www.cumulosoftware.com. Libraries and samples in many programming languages are also supplied.

Drupal and PubMed

If you are interested in running a Drupal site with PubMed content you should check the screencast below. It explains how it can be done with existing Drupal modules. I'm working with a student from the University of Szeged on a PubMed module for Drupal. So in the future this should become a bit more straightforward ;)

python 2.6 will implement a new data format (named_tuple). Can it be of use for biopython?

python 2.6 is going to implement a new kind of data (like lists, strings, etc..) called 'named_tuple'.
It is intended to be a better data format to be used when parsing record files and databases.

You can download the recipe from here (it should be included experimentally in python 2.6):
- http://code.activestate.com/recipes/500261/

Basically, you instantiate a named_tuple object with this syntax:

> Person = NamedTuple("Person name surname")

"Person" is a label for the named_tuple; the following fields, 'name' and 'surname'

Science blogging at the Royal Institution, London

sciblogNature Publishing Group are organising a workshop on science blogging, this Saturday 30th August 2008 at the Royal Institution of Great Britain in London. Why would you care? Because there are:

  1. Lots of interesting people...
  2. ...talking about a range of interesting subjects ...
  3. .. in a distinguished venue that has recently been refurbished. It is also home to the fantastic Christmas lectures and much more besides.

To cap it all, I think it will be great fun too. So if you're going, see you there. If you're not, it is never too late to publish your fantasy science funding entry. Much of the conference will be televised and blogged, making it available online too.

Let's play Fantasy Science Funding!

Donald Trump and Melania by Boss TweedFantasy Science Funding is a fun game that anybody can play. You select a Science funding body of your choice, imagine yourself as its all powerful chief executive, and decide which areas of scientific research you would "hire and fire". What could be easier? Here is how Fantasy Science Funding works...

How History Affects Pattern Matching Inside The Genome

In a recent Science magazine article, Löytynoja-Goldman showed that all current Multiple Sequence Alignment algorithms – the bread-and-butter algorithm for biologists studying similarities in genes across different species – completely fail to detect independent insertions in the alignment of sequences, and thus, erroneously mismatches regions of evolutionary volatility. In their improved MSA algorithm, PRANK, they use history itself to improve the performance of this basic algorithm. [more...]

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