iitzco / bioinformatics

Bioinformatics Visualization

Data visualization which shows similar species with a given mRNA sequence (GenBank format) or protein (fasta format).

Implemented using BioRuby, Cuba Framework, D3.js and Google Search API.

By performing a blastp with the SwissProt DB, the algorithm finds the best scoring matches and looks for the corresponding species with the accession number in the UniProtKB DB. After that, it displays the image of the best matching species in a TreeMap, where the size is proportional to the matching score.

In order to execute the WebApp, clone or download this repository and change directory (cd) to it. You'll need the following gems:

• Cuba
• Tilt
• Bio

To install the gems, execute:

$ sudo gem install cuba

$ sudo gem install tilt

$ sudo gem install bio

After that, execute:

$ rackup -p 9090

Go to http://localhost:9090

As an example, the input could be:

>gi|386828|gb|AAA59172.1| insulin [Homo sapiens] MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Which is the fasta protein of the human insulin.

Note: the size input is the quantity of species to be shown in the treemap

This was the final project of Bioinformatics course, at ITBA.

Made By:

• Ivan Itzcovich
• Kevin Kraus
• Kevin Hanna