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CBS >> CBS Biotools >> Seq2Logo-1.0

Seq2Logo-1.0 server

Seq2Logo is a web-based sequence logo ethod 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.

Note that Seq2Logo as default includes a pseudo count correction for low counts. This means that the amino acid frequencies displayed in the sequence logos are corrected for low number of observations using a Blosum amino acid similarity matrix. To turn this feature off, the Weight on prior must be set to zero.
Instructions Output format Article abstract
0) { $inpaste = trim(_INPUT("INPASTE")); } else { $inpaste = ""; } $webdir = "/biotools/Seq2Logo-1.0/bin/" // FORM HANDLER ENDS ?>

SUBMISSION

Paste input ( MSA( Fasta and ClustalW ), peptide, Weight matrix, Blast matrix )
*if left empty, the raw peptide alignment will be used as test alignment

or submit a file directly from your local disk:

Select Logo type:

Clustering method:

Specify threshold for clustering (Hobohm1) Threshold (Hobohm1)

Weight on prior (pseudo counts):

Unit Type:

Available Output Formats. (multi)

Instructions: Simply paste you alignment file in the appropriate box, choose your logo type, clustering method, weight on prior and file format and submit.

Advanced Settings 

Graphical Layout

Stacks Per Line: Lines per page:
Page size. either "A4" or as [width]x[height]:
Title (optional):

Graph Layout. (multi)

Amino Acids Colors:
Choose a coloring scheme, or assign the amino acid color manually.
Black is default if the amino acid is unassigned.
Red:
Green:
Blue:
Yellow:
Purple:
Orange:

Learn how to make an easy transfer of alignment files from your program or webpage to Seq2Logo

Confidentiality: The sequences are kept confidential and will be deleted after processing.

CITATIONS

For publication of results, please cite:

  • 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. Martin Christen Frolund Thomsen; Morten Nielsen, Nucleic Acids Research 2012; doi: 10.1093/nar/gks469.
    Abstract
    Full text


GETTING HELP

Scientific problems:        Technical problems and suggestions:       

This file was last modified Wednesday 3rd 2012f October 2012 14:18:01 GMT