Sentence examples for using the sequence logo from inspiring English sources

A logo was generated using the sequence logo software [31] available at http://weblogo.berkeley.edu/logo.cgi.edu/logo.cgi

Amino acid conservation at every position of the peptide sequence alignment was plotted using the "sequence logo" method [79], by pasting the alignment at the logo website (http://weblogo.berkeley.edu/logo.cgi, [80]).

We suggest using the sequence logo technique to understand the distribution of each the spacer sequences used in the spoligotype assay.

The presence of leucine zipper motif immediately following the homeodomain in HD-Zip III and IV sequences was confirmed using the sequence logos (Additional file 3: Figure S3, Additional file 4: Figure S4).

Authors' response: We used the Sequence Logo representation [ 89 ], a popular tool for illustrating multiple alignments of large numbers of sequences, for these figures (Figs. 9 and 10 in the revised manuscript).

Next, we used the "Sequence Logo" method developed by Stephens and Schneider [ 16] and the expression of Hertz and Stormo [ 17] to determine the information content in the Euascomycetes rRNA introns and exon flanking sequence.

To further quantify position-specific residue propensities, we plotted a sequence logo using the P10P10' sequences and constructed a heatmap of Px scores from the same dataset (as shown in Figures 1 and 2 respectively).

A total of 118 elements with intact TSD, including 90 complete TRIM elements and 28 solo-LTRs, were used to generate the sequence logo with Weblogo 3 (http://weblogo.threeplusone.com).com

Motifs in MochiView are visualized as logos, using a format based on the sequence logo design originally described by Schneider and Stephens [ 10].

Note that in the text descriptions, U is used for RNA, but T (for DNA or genes) is used as the default in the sequence logo (seqlogo) graphs.

Consequently, the number of reads used to plot each column of the sequence logo is different (shown in Additional file 6).