Sequence alignment visualization is widely applied. Interactive capabilities, hyper-links, balloon messages and the option to shield annotations and sequences become increasingly important in the ‘omics-era. Java brought interactivity to web pages and has been successfully used for the visualization of sequence alignments. However, the Java runtime-environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for many tasks render Java unnecessary.
Alignment-to-html is the first HTML5 and JavaScript based interactive visualization platform for multiple sequence alignments. Alignment rendering and the user interface is implemented in JavaScript which is natively supported by all browsers. Since Java does not need to be loaded, alignments are rapidly displayed. Only for additional display options, Java needs to be activated: 3D-visualization, phylogenetic trees and Jalview.
Each participant will use a protein family of their own choice to create decorated interactive multiple sequence alignments within an intuitive graphical user interface. Some participants may be interested in non-interactive automated alignment rendering for alignment visualization for web services. They can use the scripting language from the command line.
The tutorial will cover:
– Similarity and diversity color modes
– Balloon texts, color and style for residue selections
– BioDAS sequence features
– Association of 3D-structures and 3D-rendering (Color, ribbons, balls, sticks, labels)
– 3D-Structure superposition
– Sequence icons
– Sequence groups
– Residue index number, number offsets, peptide fragments, PDB-residue number
– Coding triplets, exon number, nucleotide index offsets
Tags: data visualization, sequence alignment, tutorial, visualization, VIZBI, VIZBI 2014