Seq2Logo: A method for construction and visualization of amino acid
binding motifs and sequence profiles including sequence weighting, pseudo
counts and two-sided representation of amino acid enrichment and depletion.
Center for Biological Sequence Analysis, Technical
University of Denmark, DK-2800 Kgs Lyngby, Denmark.
Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical
representation of the information content stored in a multiple sequence
alignment (MSA) and provide a compact and highly intuitive representation of the
position-specific amino acid composition of binding motifs, active sites, etc.
in biological sequences. Accurate generation of sequence logos is often
compromised by sequence redundancy and low number of observations. Moreover,
most methods available for sequence logo generation focus on displaying the
position-specific enrichment of amino acids, discarding the equally valuable
information related to amino acid depletion. Seq2logo aims at resolving these
issues allowing the user to include sequence weighting to correct for data
redundancy, pseudo counts to correct for low number of observations and
different logotype representations each capturing different aspects related to
amino acid enrichment and depletion. Besides allowing input in the format of
peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing
easy access for non-expert end-users to characterize and identify functionally
conserved/variable amino acids in any given protein of interest. The output from
the server is a sequence logo and a PSSM. Seq2Logo is available at