178 lines
10 KiB
Text
178 lines
10 KiB
Text
<!DOCTYPE html>
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<!-- $Id: index.html 47569 2023-09-26 20:00:30Z borodine $ -->
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<title>NCBI Multiple Sequence Alignment Viewer 1.25.3</title>
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main { font-size: 1.4em; padding-left: 2rem;}
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html { font-size: 10px; font-family: Roboto,sans-serif; }
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</head>
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<body >
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<div id="header"></div>
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<nav class="ncbi-topnav">
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<ul class="ncbi-topnav-list">
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<li><div tabindex="0" role="link" aria-label="Current page">NCBI MSA Viewer 1.25.3</div><div></div></li>
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<li><a href="/tools/msaviewer" target="_blank">Help</a></li>
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<li><a href="/tools/msaviewer/release-notes" target="_blank">Release Notes</a></li>
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</ul>
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</nav>
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<main id="main_content" accesskey="3">
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<div id="MultiAlignViewerFrame" class="MultiAlignViewerFrame" style="padding-top:17px;">
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<div id="MultiAlignViewerTitle" class="MultiAlignViewerTitle"></div>
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<div id="MultiAlignViewerTitleID" class="MultiAlignViewerTitleID"></div>
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<div id="MultiAlignViewer" class="MultiAlignViewerApp" data-autoload data-bottom=80><a href="?appname=ncbi_msav"></a></div>
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</div>
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<div id="app-frontpage" style="display:none;">
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<h1>NCBI Multiple Sequence Alignment Viewer</h1>
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<p>The NCBI Multiple Sequence Alignment Viewer (MSA) is a graphical
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display for nucleotide and protein sequence alignments.</p>
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<h3>Review <a href="/tools/msaviewer" target="_blank">documentation</a> or watch <a href="https://www.youtube.com/watch?v=ILAoBRE9eSA" target="_blank">a video tutorial</a>.</h3>
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<p>To see your own alignment, <input type="button" id="mainshow-btn" background-image = "images/upload.png" background-repeat = no-repeat background-position = left padding-left=16px
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value="Upload" onclick="location.href='?appname=ncbi_msav&openuploaddialog'"/> your data</p>
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<div onclick="this.nextElementSibling.style.display='block'; this.style.display='none'" style="position:relative;height:360px">
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<div style="position:absolute;top:0px;left:0px;">
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<img src="images/MSA_landing_picture.png" alt="Sample MSA Viewer" style="cursor:pointer;">
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</div>
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<div style="position:absolute;top:155px;left:300px;cursor:pointer;">
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<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="80px" height="60px" viewbox="0 0 500 350">
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<path
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style="fill:#bfc1c2;fill-opacity:1;fill-rule:evenodd"
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d="M 500,74.76667 C 500,33.47222 466.55,0 425.27778,0 H 74.722222 C 33.45,0 0,33.47222 0,74.76667 V 275.23333 C 0,316.52778 33.45,350 74.722222,350 H 425.27778 C 466.55,350 500,316.52778 500,275.23333 V 74.76667 z M 200,259.57778 v -188.3 l 142.78889,94.15 L 200,259.57778 z"/>
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<path
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style="fill:#949798;fill-opacity:1;stroke:none"
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d="m 199.92783,71.05723 0.0736,188.53597 142.98016,-94.18138 z"/>
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</svg>
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</div>
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</div>
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<div style="display:none">
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<!-- Embed code here -->
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<iframe width="640" height="360" src="https://www.youtube.com/embed/ILAoBRE9eSA" frameborder="0" allow="autoplay; encrypted-media;" allowfullscreen></iframe>
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</div>
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<h3>Examples of various alignment styles:</h3>
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<ul style="line-height:1.4">
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<li><a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/protein.gbp">Protein alignment with no anchor set</a></li>
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<li>
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<a href="?anchor=ACI28628&url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/protein.gbp">Protein alignment, anchor set to ACI28628</a>
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</li>
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<li>
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<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/kinases_100_seq_updated.aln">Protein alignment using FASTA format from the MUSCLE program</a>
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</li>
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<li>
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<a href="?rid=MJFN70DX013">Nucleotide alignment from Blast RID with query set as anchor; primate genomic, mRNA, and BAC sequences</a>
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</li>
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<li>
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<a href="?rid=MJRDFGTD013">Protein alignment from Blast RID, metazoan proteins belonging to the LIN37 protein family</a>
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</li>
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<li>
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<a href="?id=AY028675.1">Alignment of prion protein gene sequences from S. cerevisiae PopSet</a>
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</li>
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<li>
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<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/d3.gbp&anchor=ABW74619">Polyprotein alignment with anchor, Dengue virus 2</a>
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</li>
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<li>
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<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/dengue_nucleotide.asn&consensus=true">Genomic alignment with consensus, Dengue virus 1</a>
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</li>
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<li>
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<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/non_canonical_Flu_nonambig.asn&coloring=nss&datasource=local">Alignment of nucleocapsid coding region, Influenza A virus (nonsynonymous substitutions coloring)</a>
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</li>
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<li>
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<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/flu_H1N3_Canada_non_ambig_consensus.fa&coloring=nss">Alignment of polymerase PB1 coding region, Influenza A virus (nonsynonymous substitutions coloring)</a>
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</li>
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</ul>
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<h3>You can also embed Multiple Sequence Alignment Viewer on your own page. Following are demo pages with embedded MSA Viewer</h3>
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<ul style="line-height:1.4">
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<li><a href="demo/demo_static.html">Static embedding</a></li>
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<li><a href="demo/demo_dynamic.html">Dynamic embedding</a></li>
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<li><a href="demo/demo_sv.html">Interaction with SV on the same page</a></li>
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<li><a href="demo/demo_events.html">MSAV event handling</a></li>
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<li><a href="demo/demo_coloring.html">Different coloring options</a></li>
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<li><a href="demo/demo_mapping.html">Alignment Coordinate transformation</a></li>
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<li><a href="demo/demo_consensus.html">Consensus parameters</a></li>
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<li><a href="demo/demo_sort.html">Sorting parameters</a></li>
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<li><a href="demo/demo_columns.html">Columns re-arranging</a></li>
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</ul>
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<h2>Compatible browsers</h2>
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<p>MS Windows: Microsoft Internet Explorer 7, Firefox 2, Firefox 3, Opera 9.5</p>
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<p>Mac OS X: Firefox 2, Firefox 3, Safari 3, Camino 1.5</p>
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<p>Linux: Firefox 2, Firefox 3</p>
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