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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden

Travis J Wheeler¹, Jody Clements, Robert D Finn

¹HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA. wheelert@janelia.hhmi.org.

BMC Bioinformatics

|January 14, 2014

Summary

Skylign is a new tool for creating sequence logos from alignments and profile hidden Markov models. It offers interactive visualizations and methods to reduce sampling bias, improving conservation pattern representation.

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Area of Science:

Bioinformatics
Computational Biology

Background:

Sequence logos are graphical representations of sequence conservation in molecular biology.
They are derived from sequence alignments or profile hidden Markov models.

Purpose of the Study:

Introduce Skylign, a unified framework for generating sequence logos.
Provide interactive logo plots for web integration.
Address sampling bias and simplify gap parameter representation.

Main Methods:

Developed a web server and software package for logo generation.
Implemented interactive features including scrolling and zooming.
Incorporated methods to down-weight redundant sequences and use informed priors.
Simplified gap parameter representation and offered alternate scaling options.

Main Results:

Skylign creates static and novel interactive logo plots.
Interactive logos allow for dynamic exploration of sequence conservation data.
The tool effectively mitigates sampling bias in sequence alignments.
Simplified representation of gap parameters enhances logo clarity.

Conclusions:

Skylign is accessible as a website, web service, and downloadable package.
Interactive logos are easily embeddable in web pages using HTML.
The tool offers a versatile solution for visualizing sequence conservation patterns.