Hi All. Eric Martz posted this announcement on the Jmol list about his new Alignment visualisation tool ! This could be another candidate for the HTML publisher mechanism.
Jim -------- Forwarded Message -------- Subject: [Jmol-users] Protein sequence alignment display/analysis: MSAReveal.Org Date: Mon, 26 Sep 2016 12:07:03 -0400 From: Eric Martz <[email protected]> Reply-To: [email protected] To: [email protected] Apologies for this off-topic message which involves Jmol only tangentially, but will hopefully be of interest to some Jmol users. Recently I wanted to view some FASTA format protein sequence alignments and was not able to find free software that made me happy. So I made MSAReveal.Org (free, open source) * 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. A more detailed overview with snapshots: http://bioinformatics.org/msareveal/help.html#overview 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. Sincerely, Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org <http://Martz.MolviZ.Org>
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