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

By Travis J. Wheeler, Jody Clements, Robert D. Finn. BMC Bioinformatics, 2014

348 citations recorded by the source corpus.

Logos 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. 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 also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. Skylign 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/89ae7164ac7648b10c3df90db19c21685ddd6f8b

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In Molecular Biology

Citations in the corpus

Dali server update (2016, methodology): “The alignment is converted to an HMMer profile and visualized by a Skylign server (24).”
The HMMER Web Server for Protein Sequence Similarity Search (2017, background): “3b. Follow advanced input options as described in Alternate Protocol 1 (steps 4 to 7).”
DALI shines a light on remote homologs: One hundred discoveries (2022, methodology): “Gap columns were inserted to the alignments according to the structural alignment, so that Sequence Logos generated from the alignments, using SkyLign (Wheeler et al., 2014), have the same length and show structurally equivalent positions in the same columns.”
The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain (2022, methodology): “The computed ClustalW alignments were input into the webtool Skylign [73]; http: //skylign.org/; accessed from 25 March to 11 December 2020) with the options “Create HMM—remove mostly-empty columns”, “Some sequences are fragments” and “information content—above background”.”
InterPro in 2022 (2022, positive): “The representative model that defines a member database signature can be visualised as a logo, using Skylign (28).”