Difference between revisions of "BLAST Visualization"

From Protein Prediction 2 Winter Semester 2014
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* The visualisation uses the biojs-io-blast module to read from a BLAST xml file (EBI format).
 
* The visualisation uses the biojs-io-blast module to read from a BLAST xml file (EBI format).
* The code is under this repository [https://github.com/xwatkins/biojs-vis-blast https://github.com/xwatkins/biojs-vis-blast]
 
   
 
==Technologies==
 
==Technologies==

Revision as of 08:34, 20 November 2014

BLAST visualization

The aim of this project is to build a BioJS component to visualise BLAST results in the context of protein information. The visualisation will display alignments in context (showing how much of the total protein is part of the alignment) alongside protein features. There should also be a way to visualise the alignment at the amino-acid level.


Description

Blast


In the figure above, the query sequence (black) is displayed over the subject (red). The part of both sequences which constitutes the alignment are positioned together. The scale of both the query and subject are represented, both showing the full length of the each sequences (numbered scales at the top and bottom of the mockup). Protein features are displayed underneath the subject.

Technical details

  • The visualisation uses the biojs-io-blast module to read from a BLAST xml file (EBI format).

Technologies

  • BioJS
  • WebGl
  • Three.js

Mockup

Sketch.png



The idea is to use a circle (rectangle or any other shape) to display the hits. In that way we probably would put the hit in the center and connect the elements of the circle with it. We would accordingly put all hits to the border of the circle and connect them with matching segment of the center. Thus maybe we have to split central query sequence into multiple segments.

  • As an experiment we will try to render it in 3D with WebGl and Three.js and maybe use the score as height.


people

  • Sebastian Wilzbach
  • Homa Rasouli