Creating graphical overview with D3
This is a follow up of the previous post where I was working with understanding and parsing the BLAST output data for creating the data layer in SequenceServer. A very critical and often demanded feature for the application was the ability to have a graphical overview of all the obtained hits. It had been sitting on project's urgent list for quite a long time and couldn't be delayed any longer. So, after having a discussion with project maintainer Priyam, I assigned this task to myself.
Understanding BLAST Output
In the last post, I mentioned about a project I was trying to work on - SequenceServer. Also, in the end I said that I would be writing about the BLAST algorithm (which is the backbone of this project) and how does it works so efficiently in producing alignments even with very long sequences. However, In this post I would like to talk about BLAST program and it's output before we go into the algorithm some time later.
Easy BLAST tool - SequenceServer
Contributing to open source is quite an exciting journey. I embarked upon this mission recently with few contributions to SequenceServer - A BLAST tool, which lets you set up custom BLAST+ server to perform BLAST queries with your own database locally through a web interface. For those who are not familiar with BLAST or Basic Local Search Alignment Tool [paper] - it is an algorithm which allows quick comparison of biological sequence information which are long strings consisting of amino acids (in case of proteins) or nucleotides (in case of nucleic acids). It is exceedingly used by biologists all over the world to study newer organisms, discovery of genes and finding similarity between proteins and so on. One can see a working instance of the tool at Ant Genomes website, maintained by one of the developers and Professor at Queen Mary University London, Yannick Wurm. He's also the overseerer of the project.
Blogging is fun!
Writing a blog and personalized webpage had been one of primary tasks on my mind for quite a long time. However, Always I was caught in some acitivity thereby preventing it to happen. Finally, after lurking through many static website generators, I decided to go ahead with the Nikola and Github Pages pair as the best combination. Static websites are easy to maintain, fun, and simply effective for most of my needs. It took some time to get hold of how these work but in the process I learned about templating engines, few javascript libraries and how they are used.
Like all my other projects, the source code for this site is also made available on Github. Obviously, whatever I have created is very premature and just a working solution. If anyone has anything to say, just drop in an email or fork the site and send me a pull request. I would be happy to accept constructive changes. In the meantime, the looks and structure of the site will be subjected to frequent modifications.
