CBS >> CBS Biotools >> Seq2Logo-1.1

Seq2Logo 1.1 server

Seq2Logo is a web-based sequence logo generation 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.

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.

Try out the new beta server, which have received a major upgrade: Seq2Logo-1.2.
See the Seq2Logo-1.2 release notes here.

Instructions

Output format

Article abstract

SUBMISSION

Paste input ( MSA( Fasta and ClustalW ), peptide, PSSM) *for more info click here.

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):

Select information content units: Text on y-axis: (the text on the y-axis can be edited at will )
Note: The PSSM of non-weight-matrix inputs will always be calculated in Bits*! *or Halfbits if chosen.

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.
Need guidet help? click here.

Advanced Settings

Minimum stack width

Starting position number NOTE! Only for MSA and peptide input.

The x-axis number interval

Select a segment

Set Y-axis range

This program uses a 20x20-matrix with Blosum62 substitution frequencies to calculate pseudo counts.
It also uses the background frequencies relating to the Blosum62 matrix.
If you prefer a different version, you can use your own by uploading them here. *PLEASE USE THE SAME FORMATS!

Blosum62 matrix

Background frequencies

Need guidet help? click here.

Graphical Layout

Stacks Per Line: Lines per page:

Page size [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:

Need guidet help? click here.

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 Thursday 11th 2013f July 2013 14:15:43 GMT

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