Abstract
The iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over- but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html.
Highlights
The development of high throughput methods for analysing oligonucleotides and proteins led to the discovery of large amounts of sequence-based information
In 1990 Schneider and Stephens described a method to visualize and analyse such conserved patterns [1]. These so-called sequence logos are histogram-like presentations where every bar is a stack of letters and are created with a group of sequences of the same length as the input
The height of a stack is calculated by Shannon’s information theory. This takes into account the maximum number of possible different residues (4 different nucleotides or 20 different amino acids) and the observed frequencies of these residues on that position in the experimental multiple sequence alignment
Summary
The development of high throughput methods for analysing oligonucleotides and proteins led to the discovery of large amounts of sequence-based information. Slogos (oligonucleotides) and Plogos (proteins) attempt to address this issue by providing the user with the ability to set a fixed frequency for every residue, and so create a corrected sequence logo still relying on Shannon’s information theory [3]. If two experimental sets are available, the differences in both overand under-represented residues can be visualized by the TwoSampleLogo web application [4].
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