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Usage Instructions



The user interface of Seq2Logo is split in 3 parts; submission, graphical layout and advanced settings.


Submission

In the submission part the user can:

  1. Upload his or hers alignment file, either by copy/paste or by choosing a local file.
  2. Specify the logo type, either Shannon, Kullback-Leibler, Weighted Kullback-Leibler, Probability Weighted Kullback-Leibler or PSSM-Logo.
  3. Choose which kind of sequence weighting should be used to reduce sequence redundancy.
  4. Assign the weight on prior value that should be used to adjust for a small alignment file (Recomended for data with less than 50 sequences).
  5. Choose the unit of the Y-axis.
  6. Choose additional formats for the logo file.

NOTE: As stated above the paste field Seq2Logo supports following alignments formats: Peptides, Fasta, Clustal and weight matrices.

The peptide format is a file where each line is a new peptide sequence, only the amino acid and gap symbols are accepted.

The Fasta format is a file where '>' describes the header line, and all following lines composes the sequence belonging to the header. Only the amino acid and gap symbols are accepted in the sequence.

The CLUSTAL format is a file where the data is separated in two or three columns, first column containing the sequence name, second column containing the sequence, and the optional third column containing the position number of the last amino acid.

The weightmatrix format is a file where the data is a PSSM, Seq2Logo needs a header line with the 20 amino acids, followed by rows of at least 20 columns (a weight for each amino acid) of numbers. Optionally the data lines can contain 2 header columns, where the first specifies the true position in the sequence and the second specifies the amino acid from the concensus sequence at the given position.

Submission


 

Graphical Layout

In the grafical layout part the user can:

  1. Assign the number of stacks per line.
  2. Assign the number of lines per page.
  3. Set the resolution of the image.
  4. Assign a logo title.
  5. Specify the layout of the graph.
  6. Choose a coloring scheme from the list.
  7. Manually assign the colors of the individual amino acids.
Graphical Layout


 

Advanced Settings

In the advanced settings part the user can:

  1. Set the minimum width for stacks with gaps (if set to 1 there is no width adjustment of the stacks to show positions where gaps occur).
  2. Set the position number of the first amino acid in the alignment.
  3. Set the frequency of which the position numbers are shown on the X-axis. (if the value is set to 1 all positions numbers are shown. If the value is left out or 0 the interval is determined automatically.)
  4. Set a segment range if only a part of the full alignment is wanted. (The only valid format is "start-end", eg. 5-56 )
  5. Upload separate substitution frequency matrix.
  6. Upload separate Background frequency file (distribution of amino acids).
Advanced Options

 


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