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Can you create a sequence logo using WebLogo?
The WebLogo tool allows you to create sequence logos based on multiple sequence alignments. However if you want to create a vector image of a sequence logo based on position frequency matrices we need another resource.
What are the input data types for ggseqlogo?
As input, ggseqlogo requires a sequence alignment as a character vector or position frequency matrix, depicting the count of each letter per position. The input data sequence type is flexible and can be one of DNA, RNA or protein ( Fig. 1d–e ), or a custom dictionary can optionally be defined to allow for non-standard logos. ( Fig. 1f ).
What are the functions of a sequence logo?
Sequence logos also play a major role in visualizing DNA, RNA and protein binding sites, such as that of kinases, SH2/SH3 domains, transcription factors (TFs), RNA-binding proteins, nucleases, the nuclear ribonucleo proteins and countless more.
How is ggseqlogo used to draw letters?
The core visualization used in ggseqlogo relies on the use of polygons to draw elongated letters in ggplot2. Letters from a font are converted to high-resolution images and traced to provide coordinates of letters in 2 D space. To compute letter heights, ggseqlogo employs one of two commonly used methods.
What do you need to know about weblogois?
WebLogois a web based application designed to make the generationof sequence logos as easy and painless as possible. A sequence logois a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence.
Which is the best file format for WebLogo?
Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP for multiple sequence alignments, and transfac for position weight matrices. All sequences must be the same length, else WebLogo will return an error and report the first sequence that differed in length from previous sequences. Output format
Is the WebLogo source code available for download?
In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence. The WebLogo source code is available for download .