MultiDisp instructions

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General

MultiDisp is a tool for analysing and visualising multiple sequence alignments (MSAs). The program generates several different plots and maps for investigating MSAs. Some of the visualisations are only for protein sequences while others work also for nucleotide sequences. MutiDisp does not constructi the necessary MSA, user needs to obtain it first with one of the numerous options available. MultiDisp is HTML5 application and uses workstation resources only. The web browser has to be capable of running HTML5 code. How fast and how large alignments user can run depends user's workstation and web browser resources.

Input

MultiDisp accepts alignments in Clustal, FASTA, MUSCLE, PROBCONS and and Stockholm (Pfam) file format. MultiDisp automatically regocnises the MSA file format. Input of alignment can be done either by downloading a file or pasting the MSA to the text area provided. If file input is chosen, then data in text area is neglected. When MSA file has been chosen or placed on text area, by clicking "Continue" button, analysis view is opened.

Analysis

Analysis view allows user to generate diffrent visualisations and analyse the given MSA. To feed a new alignment, click "Cancel" to go back to the Input view.

Project title and alignment name/comment

Information to be presented on all the outputs can be provided e. g. for the name and details of alignment.

Select area

The analysed area of the MSA can be chosen with this option.

Character heights

Character height graphsare images, where each character in a column for MSA is drawn based on it's relative frequency as the height. If relative amount of a character is so small to not be visible, it is not drawn at all. If the MSA is very large, containing at least hundreds of sequences, then web browser may give a warning:

A script on this page may be busy, or it may have stopped responding. You can stop the script now, open the script in the debugger, or let the script continue.

Many web browsers monitor scripts and prevent jamming. In this situation user must choose continue. Another option is to analyse the alignment in slices.

Sorting order

This options sets the sorting order of characters. The choices are Alphabetical and By ratio.

Colouring scheme

There are three Character colouring options.

Normal
Similar residues have same color
By residue
Each residue has it's own colour
Conservation gradient
Conservation degree defines the colour.

Draw image

Clicking this button generates the image. When image is ready, it appears on screen. Character heights images can be saved as PNG or PDF files.

Maps

Maps are used to visualise physicochemical properties of amino acids in the alignment positions. The idea is same as in character images, but instead of character the propensity value of amino acids is drawn with color coding. The higher the frequency of the amino acid the higher the bar for the propensity value is in the map. Maps are available for three properties and hydropathy and polarity with several propersity scales.

Average area buried
Visualises the average area buried values of residues. Each value has it's own color based on [Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H., Science 229:834-838(1985)].
Hydropathy
Visualises hydropathy values of residues. Each value has it's own color. Score tables are the same as in hydropathy plot. Positive values are drawn with red bar and negative values with blue bar. The scales are normalized[Satu Jääskeläinen, Pentti Riikonen and Tapio Salakoski,Accuracy of protein hydropathy predictions Int. J. Data Mining and Bioinformatics, Vol. 4, No. 6, 2010]. Hydropathy scales included are
Polarity
Visualises polarity of residues in MSA alignment positions. Each value has it's own color. Polarity scales included are

Plots

There are four plots to indicate similarity in the alignment positions plus two plots, those fro hydropathy and polarity, to show trends in amino acid propensities.

Variability
Bar chart, where bar height shows variability in the MSA columns. Here variability is defined as a number of different amino acids divided by the amount of most frequent amino acid.
Identity
Bar chart, where bar height shows degree of seqeunce identity in MSA columns.
Similarity
Like identity, but similar residues are considered as the same inside the group. Groups used in MultiDisp are [A,G,H], [C,S,Y], [D,E,G,N,Q] and [F,I,L,W,Y,K,M,R].
Entropy
Entropy (information content) [Shannon, C.E., Weaver, W., 1963. The Mathematical Theory of Communication. University of Illinois Press, Champaign, IL.] in MSA columns.
Hydropathy
Calculates sum of hydrophobicity prediction in the columns with chosen hydropathty scale. The plot can be generated by smoothing the values over sequence positions by using sliding window. The optimal window size 9 is selected by default [Satu Jääskeläinen, Pentti Riikonen and Tapio Salakoski,Accuracy of protein hydropathy predictions Int. J. Data Mining and Bioinformatics, Vol. 4, No. 6, 2010] ] but can be changed from 1 to 21.
Polarity
Calculates sum of polarity in the columns with chosen polarity scale and with sliding window. Positive values are drawn with red bar and negative with blue bars.

Saving images on files

Besides the image view, there is a button panel for saving the images as files in PNG or PDF format. PNG image is exactly like the image seen on the screeb, while PDF image is scaled to fit to one or more A4 pages. By default, the images are saved to the download folder. If the alignment is longer than 3000 residues the PDF plots and maps may become difficult to read, because plots and maps are always scaled to one page. In such case draw the images piecewise by selecting area instead of the full MSA. Character images will produce multiple pages if the alignment is longer than 320 positions.