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.
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 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.
Information to be presented on all the outputs can be provided e. g. for the name and details of alignment.
The analysed area of the MSA can be chosen with this option.
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:
Many web browsers monitor scripts and prevent jamming. In this situation user must choose continue. Another option is to analyse the alignment in slices.
This options sets the sorting order of characters. The choices are Alphabetical and By ratio.
There are three Character colouring options.
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 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.
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.
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.