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    Resources: Protein sequence alignment display/analysis with MSAReveal.Org
    Submitted by Eric Martz; posted on Monday, September 26, 2016


    MSAReveal.Org is a new, free, open-source website for display and analysis of your protein sequences and sequence alignments:

    # Paste in protein sequences or alignments in FASTA format.
    # Genus and species, gene names, and UniProt IDs are extracted from the headers and tabulated. UniProt IDs are linked to UniProt.
    # Checkboxes control coloring of amino acids/groups.
    # Touching an amino acid reports its 3-letter abbreviation and sequence number in a tooltip. You don't have to memorize all 20 one-letter amino acid codes.
    # The sequence listing can be horizontally scrolled, or wrapped at a specified number of amino acids.
    # A sequence numbering offset can be specified with "start=N" in the header of each sequence. A negative number enables numbering to start at 1 for the mature protein, after a negatively numbered signal sequence.
    # A consensus is reported with the frequencies of amino acids in each column.
    # Statistics are tabulated including lengths (excluding gaps), percentages identity, percentages in gaps, percentages charged, percentages aromatic, net charge at neutral pH, etc. etc..
    # Minimum, average, and maximum are given for each column in Statistics.
    # The Statistics Table can be sorted on any column.
    # A search mechanism finds and highlights sequence fragments/motifs regardless of gaps. It accepts multiple amino acid possibilities at a given position.
    # Search hits are listed with links so you can jump to any hit instantly.
    # Numerous irregularities or warnings are reported, including the ambiguous codes B, J, O, U, X, Z and illegal characters, which can be located easily with the search mechanism.
    # A description of each alignment, added to the first header, will be displayed.
    # A description of each sequence, added to its header, will be displayed when its taxon is touched.
    # A Protein Data Bank ID, when added to the header (e.g. "PDB=2ace") will be tabulated and linked to display the 3D model in FirstGlance.Jmol.Org.
    # New in September, 2016.

    A more detailed overview with snapshots:

    Demonstration and test alignments are built in. Instructions are provided for downloading sequences from UniProt, and aligning them with free, easy, quick Jalview (using MAFFT, TCOFFEE, MUSCLE, etc.). Displays any FASTA alignments, e.g. from the ConSurf Server. MSAReveal.Org works in all popular browsers, Windows or OS X. Tested up to a total of one million amino acids, and with alignments containing hundreds of sequences.

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