Abstract
BackgroundLogos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position.ResultsWe present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.ConclusionSkylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign’s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at http://skylign.org.
Highlights
Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences
Alignments and profile hidden Markov models Alignments of multiple biological sequences play an important role in a wide range of bioinformatics applications, and are used to represent sequence families that range in size from DNA binding site motifs to full length proteins, ribosomal RNAs, and autonomous transposable elements
Because profile HMMs create positions only for consensus columns, and because a logo stack is defined only for non-empty alignment columns, not all columns in an alignment will be represented by a position in a profile logo; Skylign optionally shows the mapping between each logo position and the corresponding column in the underlying alignment
Summary
We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position
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