WebLogo: A Sequence Logo Generator: Figure 1

Abstract

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.Sequence logos were invented by Tom Schneider and Mike Stephens (Schneider and Stephens 1990;Shaner et al. 1993) to display patterns in sequence conservation, and to assist in discovering and analyzing those patterns. As an example, the accompanying figure (Fig. 1) shows how WebLogo can help interpret the sequence-specific binding of the protein CAP to its DNA recognition site (Schultz et al. 1991). Homodimeric DNA-binding proteins typically display a symmetric double hump in the DNA binding-site logo (Schneider and Stephens 1990), as shown in the figure. Deviations from this basic pattern can indicate additional features; a highly conserved residue in the center of such a pattern may indicate DNA distortion or base flipping (Schneider 2001); an unexpectedly high-sequence conservation may be due to overlapping binding sites (Schneider et al. 1986). Protein logos can illuminate patterns of amino acid conservation that are often of structural or functional importance (Galperin et al. 2001;Rigden et al. 2003). Sequence logos have also been used to display patterns in the BLOCKS protein sequence database (Henikoff et al. 1995), and in DNA-binding site motifs (Robison et al. 1998;Nelson et al. 2002), to analyze splice sites (Stephens and Schneider 1992;Emmert et al. 2001), and in a variety of other contexts. Additional examples, and the raw data for the example presented here, can be found on the WebLogo examples page (http://weblogo.berkeley.edu/examples.html).The logo generation form (http://weblogo.berkeley.edu/ logo.cgi) can process RNA, DNA, or protein multiple sequence alignments provided in either FASTA (Pearson and Lipman 1988) or CLUSTAL (Higgins and Sharp 1988) formats. If the user does not explicitly specify the sequence type, then WebLogo will make a determination on the basis of the symbols found within the sequences. A logo represents each column of the alignment by a stack of letters, with the height of each letter proportional to the observed frequency of the corresponding amino acid or nucleotide, and the overall height of each stack proportional to the sequence conservation, measured in bits, at tha...

Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes

“…754 L10 sequences formed the target sample that represented 42,000 individual sequences. Sequence logos were created using WebLogo server 48 , using the chemistry colour scheme. A search of the NCBI database for organellar L10 sequences yielded 82 mitochondrial and 29 chloroplastic sequences that could be unambiguously annotated.…”

Opening of the human epithelial calcium channel TRPV6

“…The selectivity filter residues in K + channels and gating hinge residues in S6 (M3 in GluA2) are colored red. k , Aligned sequence logos for TRPV channels in S6, generated by WebLogo 50 from 1200 TRPV1–6 sequences. The red rectangle and arrow indicate the position of the alanine gating hinge in TRPV6.…”

New CRISPR–Cas systems from uncultivated microbes

“…Hits belonging to contigs that contained an associated repeat were filtered out (to avoid identifying CRISPR arrays as protospacers). Protospacer adjacent motifs (PAMs) were identified by aligning regions flanking the protospacers and visualized using WebLogo 55 . In cases that one spacer had multiple putative protospacers with different composition of flanking nucleotides, each distinct combination of protospacer and downstream nucleotides was taken into account for the logo calculation.…”