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UME User's manual
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="UME User's manual" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/ume-e.html" /> <meta property="og:description" content="UME (Utilities for MSS file Error check) is a stand-alone GUI tool to check synt..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>UME User's manual</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="ddbj"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; height: 40px;" data-bottom-menu="true" data-ddbj-home-page="true" data-search="true" ></script> <section class="top-news-view"> <div class="inner"> <ul> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-10-22-e">On Cyber Threats against DDBJ, a node of the International Nucleotide Sequence Database Collaboration</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-11-22-e">(27th November 9:00-November 28th 12:00)Announcement of D-way/MSS suspension</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/">(12th December 8:00-20th December 12:00(JST)) Suspension of DDBJ services due to NIG supercomputer maintenance</a> </li> </ul> </div> </section> <div id="primary"> <header id="PageHeader"> <div class="inner"> <div class="page-title"> <p class="title -normal">DDBJ Annotated/Assembled Sequences</p> </div> <nav class="tab-menu-view"> <ul class="tabmenucontainer"> <li class=" -current"> <a href="/ddbj/index-e.html">Home</a> </li> <li class=" -haschild"> <a href="/ddbj/submission-e.html">Submission</a> <ul> <li> <a href="/ddbj/submission-e.html">Before Submission</a> </li> <li> <a href="/ddbj/web-submission-e.html">Web submission</a> </li> <li> <a href="/ddbj/mss-e.html">Mass Submission</a> </li> <li> <a href="/ddbj/update-e.html">Data Update</a> </li> </ul> </li> <li class=" -haschild"> <a href="http://ddbj.nig.ac.jp/arsa/?lang=en">Search</a> <ul> <li> <a href="http://getentry.ddbj.nig.ac.jp/top-e.html">getentry</a> </li> <li> <a href="http://ddbj.nig.ac.jp/arsa/?lang=en">ARSA</a> </li> </ul> </li> <li class=" -haschild"> <a href="/ddbj/flat-file-e.html">Flat file</a> <ul> <li> <a href="/ddbj/feature-table-e.html">Feature Table</a> </li> <li> <a href="/ddbj/features-e.html">Feature key</a> </li> <li> <a href="/ddbj/qualifiers-e.html">Qualifier key</a> </li> <li> <a href="/ddbj/sequence-e.html">Nucleotide Sequences</a> </li> <li> <a href="/ddbj/organism-e.html">Organism qualifier</a> </li> <li> <a href="/ddbj/identifiers-e.html">Identifiers</a> </li> <li> <a href="/ddbj/location-e.html">Description of Location</a> </li> <li> <a href="/ddbj/cds-e.html">Protein Coding Sequence</a> </li> <li> <a href="/ddbj/geneticcode-e.html">The Genetic Codes</a> </li> <li> <a href="/ddbj/code-e.html">Codes Used in Sequence Description</a> </li> <li> <a href="/ddbj/example-e.html">Description Examples of Sequence Data</a> </li> </ul> </li> <li class=" -haschild"> <a href="/ddbj/data-categories-e.html">Data categories</a> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/pseudohaplotype-e.html">Pseudohaplotype</a> </li> <li> <a href="/ddbj/wgs-e.html">WGS</a> </li> <li> <a href="/ddbj/finished_level_genome-e.html">Finished level genomic sequences</a> </li> <li> <a href="/ddbj/metagenome-assembly-e.html">Metagenome Assembly</a> </li> <li> <a href="/ddbj/single-amplified-genome-e.html">Single amplified genome</a> </li> <li> <a href="/ddbj/htg-e.html">HTG</a> </li> <li> <a href="/ddbj/environmental-e.html">Environmental sample</a> </li> <li> <a href="/ddbj/env-e.html">ENV</a> </li> <li> <a href="/ddbj/tls-e.html">TLS</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tsa-e.html">TSA</a> </li> <li> <a href="/ddbj/est-e.html">EST</a> </li> <li> <a href="/ddbj/htc-e.html">HTC</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </li> <li class=""> <a href="/faq/en/index-e.html?tag=ddbj">FAQ</a> </li> <li class=" -haschild"> <a href="/ddbj/index-e.html">Other</a> <ul> <li> <a href="/ddbj/patent-data-e.html">Patent</a> </li> <li> <a href="/ddbj/mga-e.html">MGA</a> </li> </ul> </li> </ul> </nav> </div> </header> <section id="NavigationAndMainView"> <div class="inner"> <div class="subview"> <nav id="TableOfContents" class="internal-link"> </nav> </div> <section id="MainContentView" class="mainview"> <header class="header"> <nav class="breadcrumb-view"> <ul> <li> <a href="https://www.ddbj.nig.ac.jp/index-e.html">Home</a> </li> <li> <a href="https://www.ddbj.nig.ac.jp/ddbj/index-e.html">ddbj</a> </li> <li><a>UME User's manual</a></li> </ul> </nav> <h1 class="title">UME User's manual</h1> </header> <main class="md-content"> <p>UME (Utilities for MSS file Error check) is a stand-alone GUI tool to check syntax and format of <a href="/ddbj/file-format-e.html#sequence">Sequence file</a> and <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> required for using Mass Submission System of DDBJ and to check amino acid translation of <a href="/ddbj/cds-e.html">CDS feature</a> based on the description of each file. UME includes both Parser and transChecker.</p> <h2 id="function">Basic function</h2> <table> <thead> <tr> <th>Name</th> <th>Functions</th> </tr> </thead> <tbody> <tr> <td><a href="#validation-2">Parser</a></td> <td>Verification of the syntax and format for <a href="/ddbj/file-format-e.html#sequence">Sequence file</a> and <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>.</td> </tr> <tr> <td><a href="#validation-3">transChecker</a></td> <td>Validation of the amino acid translation for <a href="/ddbj/cds-e.html">CDS (protein-coding sequence)</a> feature.</td> </tr> <tr> <td><a href="#validation-4">FFconv</a></td> <td>Making simulated format of <a href="/ddbj/flat-file-e.html">DDBJ flat file</a> from <a href="/ddbj/file-format-e.html#sequence">Sequence file</a> and <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>.</td> </tr> <tr> <td><a href="#agpparser">AGPParser</a></td> <td>For the submission of contigs (<a href="/ddbj/con-e.html">CON entries</a>), <a href="/ddbj/file-format-e.html#agp">AGP file</a> and <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>.</td> </tr> </tbody> </table> <h2 id="install">Install</h2> <p>Download UME package from <a href="/ddbj/mss-tool-e.html">Validation tool for MSS data file</a>.<br /> Uncompress the downloaded file to extract its contents into the UME folder.</p> <dl> <dt>Windows: Uncompress UME_win.zip</dt> <dd>In case of Windows, you can likely explore the files packed in zip format, directly, like as a folder. However, to run UME, all files in the UME package must be uncompressed.</dd> <dt>unix/macOS: Uncompress UME_unix.zip</dt> <dd>Extract the zipped file using a decompression program or the following command.</dd> </dl> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>$ gunzip UME_unix.zip </code></pre></div></div> <dl> <dt>macOS: Regarding the available file names</dt> <dd>DO NOT use multibyte character(s) for any file or folder name of <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>, <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>, or <a href="/ddbj/file-format-e.html#agp">AGP file</a> when you use UME on some versions of macOS. UME may not work when multibyte character is included in the file or folder name.</dd> </dl> <h2 id="initial">Initialization</h2> <h3 id="initial-1">Starting UME</h3> <p>You can run UME application by double clicking the UME icon (Depending on your PC environment, some extension of UME file would be displayed) in the UME folder.</p> <p>On macOS, you may not be able to run UME by double clicking the icon.<br /> In that case, please run UME by typing commands on Terminal window like as follows.</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>$ cd UME # Move to directory that you have expanded UME package. $ ./UME.sh </code></pre></div></div> <p><img src="/assets/images/ddbj/UME1-e.png" alt="Starting UME" title="" class="" /></p> <dl> <dt>lib folder</dt> <dd>Directory which includes library files used by UME. <br /> If you move this directory or any file in it, UME would not properly work.</dd> <dt>resource folder</dt> <dd>Directory which includes resource files used by UME. <br /> If you move this directory or any file in it, UME would not properly work.</dd> <dt>sample folder</dt> <dd>Including sample files for DDBJ submission.</dd> <dt>UME file</dt> <dd>Start UME application by double-clicking this file.</dd> <dt>license file</dt> <dd>A text file for license agreement. Please read at first. The contents of the file are the same as <a href="/ddbj/mss-tool-e.html#license">End-user license agreement</a>.</dd> </dl> <h3 id="initial-2">Initial setting of UME</h3> <p>At the first time, you run UME application, change the maximum size of RAM for UME to optimize run-time environments. <br /> The default configuration of it is 512 Mbytes.</p> <p><a href="/assets/images/ddbj/UME2.png"><img src="/assets/images/ddbj/UME2.png" alt="" /></a></p> <p>(1) Click Config in menu bar. <br /> (2) Select the appropriate size of Max memory for runtime from pull-down menu.</p> <h2 id="validation">Verification of submission files</h2> <h3 id="validation-1">Check panel: basic verification of submission files</h3> <p>You can move to this panel by clicking the Check tab enclosed in the red square.</p> <p><img src="/assets/images/ddbj/UME3.png" alt="Check panel: basic verification of submission files" title="" class="" /></p> <p>(1) Specify the subjects, both <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>. <br /> (2) By clicking Execute button, verify the files specified at step (1) by Parser. <br /> (3) By clicking Execute button, validate amino acid translation of the files specified at step (1) by transChecker. <br /> (4) By clicking Execute button, process the files specified at step (1) by FFconv. <br /> (5) By clicking Exit button, Close UME.</p> <h3 id="validation-2">Parser: verification of syntax and format</h3> <p>Execute Parser through the following steps.</p> <p><img src="/assets/images/ddbj/UME5.png" alt="Parser: verification of syntax and format" title="" class="w600" /></p> <p>Click Check tab and move to Check panel.</p> <p>(1) Specify the subjects, both <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>. <br /> (2) By clicking Execute button, process the files specified at step (1) by Parser. <br /> (3) When you check the box, Save log in file, the result log of Parser is saved as a text file. <br /> (4) The window of Parser log is opened. <br /> (5) The progress of Parser is indicated. <br /> (6) The result log of Parser is displayed. <br /> (7) By clicking Save button, the contents of (6) are saved as a text file. <br /> (8) By clicking Close button, the window, Parser result, is closed.</p> <div class="attention"> <p>When an error occurs, the parser outputs an error message. <br /> Please reffer: <a href="/ddbj/validator-e.html#Parser">Parser Error Eessages</a>, in detail.</p> </div> <h3 id="validation-3">transChecker: validation of amino acid translation</h3> <p>transChecker can translate nucleotide sequences of <a href="/ddbj/file-format-e.html#sequence">Sequence file</a> into amino acid sequences corresponding to <a href="/ddbj/cds-e.html">CDS features</a> specified at Annotation file. <br /> Before using transChecker, both two files should be checked by <a href="#validation-2">Parser</a>, and remove all of Parser errors. <br /> Please note that when some Parser error is found, transChecker is terminated without any result. Execute transChecker through the following steps.</p> <p><img src="/assets/images/ddbj/UME6.png" alt="transChecker" title="" class="w600" /></p> <p>Click Check tab to move to Check panel.</p> <p>(1) Specify the subjects, both <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>. <br /> (2) By clicking Execute button, process the files specified at step (1) by transChecker. <br /> (3) When you check the box, Save log in file, the execution log and error messages of transChecker are saved as a text file. <br /> (4) When you check the box, Save translated sequences in file the amino acid sequences translated by transChecker are saved as a text file in either of two formats. <br /> 聽聽聽聽聽You can specify the format for translated amino acid sequences from following two types.</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>| [FASTA-like format](/ddbj/transchecker.html#output-1-1) | in case of selecting Translate in FASTA format | | [Alignment with nucleotide sequence](/ddbj/transchecker-e.html#output-1-2) | in case of selecting Translate in alignment with nucleotide sequence | </code></pre></div></div> <p>(5) The window of transChecker is opened. <br /> (6) The progress of transChecker is indicated. <br /> (7) The execution log and error messages of transChecker are displayed. <br /> (8) By clicking Save button, the contents of (7) are saved as a text file. <br /> (9) The amino acid sequences translated by transChecker are displayed in the format selected at (4). <br /> (10) By clicking Save button, the contents of (9) are saved as a text file. <br /> (11) By clicking Close button, the window, transChecker result, is closed.</p> <div class="attention"> <p>When an error occurs, the transChecker outputs an error message.<br /> Please reffer: <a href="/ddbj/validator-e.html#transChecker">transChecker Error Eessages</a>, in detail.</p> </div> <h3 id="validation-4">FFconv: confirmation by making simulated DDBJ flat file</h3> <p>FFconv can make simulated format of <a href="/ddbj/flat-file-e.html">DDBJ flat file</a> from <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>.</p> <p>Before using FFconv, both two files should be checked by , and remove all of Parser errors. Please note that when some Parser error is found, FFconv is terminated without any result.</p> <p>Execute FFconv through the following steps.</p> <p><img src="/assets/images/ddbj/UME7.png" alt="FFconv" title="" class="w600" /></p> <p>Click Check tab to move to Check panel.</p> <p>(1) Specify the subjects, both <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>. <br /> (2) By clicking Execute button, make simulated format of DDBJ flat file from the files specified at step (1) by FFconv. <br /> (3) When you check the box, Save flat file in file, the result of FFconv, simulated format of DDBJ flat file, is saved as a text file. <br /> (4) The window of FFconv result is opened. <br /> (5) The progress of FFconv is indicated. <br /> (6) The execution log of FFconv is displayed. <br /> (7) By clicking Save button, the contents of (6) are saved as a text file. <br /> (8) The result of FFconv, simulated format of DDBJ flat file, is displayed. <br /> (9) By clicking Save button, the contents of (8) are saved as a text file. <br /> (10) By clicking Close button, the window, FFconv result, is closed.</p> <h2 id="agpparser">Verification of contig submission files</h2> <p><span class="red"><strong>[Caution] DDBJ currently terminated accepting new submissions.</strong> </span></p> <h3 id="panel-2">Contig panel: verification of AGP file for contig submission</h3> <p>You can move to this panel by clicking the Contig tab enclosed in the red square.</p> <p><img src="/assets/images/ddbj/UME4.png" alt="Verification of contig submission files" title="" class="" /></p> <p>(1) Specify the subject, <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>. <br /> (2) Specify the subject, <a href="/ddbj/file-format-e.html#agp">AGP file</a>. <br /> (3) Specify the subject, Multi-fasta file for components in AGP file. <br /> (4) By clicking Execute button, process the files specified at steps (1) to (2) by AGPParser. <br /> (5) By clicking Exit t button, Close UME.</p> <h3 id="agpparser-1">Executing AGPParser</h3> <p>Basically, AGPParser checks the format of <a href="/ddbj/file-format-e.html#agp">AGP file</a>.AGP file. <br /> When you specify <a href="/ddbj/file-format-e.html#annotation">Annotation file</a> and/or multi-fasta file including all of sequences cited by AGP file, AGPParser also checks the consistency between the two or three files.</p> <p><img src="/assets/images/ddbj/UME8.png" alt="Executing AGPParser" title="" class="w600" /></p> <p>Click Contig tab to move to Contig pannel.</p> <p>(1) Specify the subject, <a href="/ddbj/file-format-e.html#annotation">Annotation file</a>. Not required. <br /> (2) Specify the subject, <a href="/ddbj/file-format-e.html#agp">AGP file</a>. Required. <br /> (3) Specify the subject, the multi-fasta file including all of sequences cited by <a href="/ddbj/file-format-e.html#sequence">Sequence file</a>. Not required. <br /> (4) By clicking Execute button,AGPParser checks the specified file at the steps (1) to (3). <br /> (5) When you check the box, [Construct sequence from AGP and multi-fasta files], AGPParser constructs <br /> 聽聽聽聽聽a text file for nucleotide sequence(s) on accordance with the specification of the two files. <br /> (6) Check the button, Save log in file,then the result log of AGPParser is saved as a text file. <br /> (7) The window of AGPParser log is opened. <br /> (8) The progress of AGPParser is indicated. <br /> (9) The result log of AGPParser is displayed. <br /> (10) By clicking Save button, the contents of (9) are saved as a text file. <br /> (11) By clicking Close button, the window of AGPParser log is closed.</p> <div class="attention"> <p>When an error occurs, the AGPParser outputs an error message. <br /> Please reffer: <a href="/ddbj/validator-e.html#AGP_Parser">AGPParser Error Messages</a>, in detail.</p> </div> </main> <aside class="related-pages"> <h2 class="caption">Related pages</h2> <div class="navigation"> <nav> <ul> <li> <a href="/ddbj/file-format-e.html">Submission File Format</a> </li> <li> <a href="/ddbj/mss-tool-e.html">Validation tools for MSS data files</a> </li> <li> <a href="/ddbj/parser-e.html">Parser User's Manual</a> </li> <li> <a href="/ddbj/transchecker-e.html">transChecker User's Manual</a> </li> <li> <a href="/ddbj/validator-e.html">Validator error message</a> </li> <li> <a href="/ddbj/mss-form-e.html">Application form for MSS</a> </li> </ul> </nav> </div> </aside> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>