Mercator4http://plabipd.de:-1/portal/web/guest/wiki/-/wiki/349982024-03-28T10:22:41Z2024-03-28T10:22:41ZVersion History 1.7Marie Bolgerhttp://plabipd.de:-1/portal/web/guest/wiki/-/wiki/34998/Version+History2021-10-04T15:25:55Z2021-10-04T15:25:55Z<h3 id="section-Version+History-Current+version"> Current version <a class="hashlink" href="#section-Version+History-Current+version">#</a></h3><p><strong>Mercator4 v4.0 - release version (October 2021)</strong> </p><ul><li>29 functional root categories (BIN-01 .. BIN-28 + BIN-30)</li><li>5201 functional leaf bin categories (including 1696 scaffold categories)</li><li>1 enzyme-class root category (BIN-50)</li><li>50 enzyme-class leaf categories (including 7 scaffold categories)</li><li>1 unknown root category (BIN-35)</li><li>2 unknown leaf categories</li></ul><ul><li>New Heatmap viewer to allow user to visualize results immediately</li></ul><h3 id="section-Version+History-Legacy+updates"> Legacy updates <a class="hashlink" href="#section-Version+History-Legacy+updates">#</a></h3><p><strong>Mercator4 v3.0 - release version (July 2020)</strong> </p><ul><li>28 functional root categories (BIN-01 .. BIN-27 + BIN-30)</li><li>4819 functional leaf bin categories (including 1601 scaffold categories)</li><li>1 enzyme-class root category (BIN-50)</li><li>50 enzyme-class leaf categories (including 7 scaffold categories)</li><li>1 unknown root category (BIN-35)</li><li>2 unknown leaf categories</li></ul><p><strong>Mercator4 v2.0 - release version (Feb 2020)</strong> </p><ul><li> Update to FASTA annotations</li></ul><p><strong>Mercator4 v2.0 - release version (July 2019)</strong> </p><ul><li>27 functional root categories (BIN-01 .. BIN-27)</li></ul><ul><li>4450 functional leaf bin categories (including 1484 scaffold categories)</li></ul><ul><li>1 enzyme-class root category (BIN-50)</li></ul><ul><li>50 enzyme-class leaf categories (including 7 scaffold categories)</li></ul><ul><li>1 unknown root category (BIN-35)</li></ul><ul><li>2 unknown leaf categories</li></ul><p><strong>Mercator4 v1.0 - release version</strong> </p><p><strong></strong> </p><ul><li>27 functional root categories (BIN-01 .. BIN-27)</li></ul><ul><li>4095 functional leaf bin categories (including 1332 scaffold categories)</li></ul><ul><li>1 enzyme-class root category (BIN-50)</li></ul><ul><li>50 enzyme-class leaf categories (including 7 scaffold categories)</li></ul><ul><li>1 unknown root category (BIN-35)</li></ul><ul><li>2 unknown leaf categories</li></ul><p><strong></strong> </p><p><strong>Mercator4 v0.3 - Beta version</strong><br/><strong></strong> </p><ul><li>27 functional root categories (BIN-01 .. BIN-27)</li></ul><ul><li>3883 leaf bins categories (including 1249 scaffold categories)</li></ul><ul><li>1 unknown root bin (BIN-35)</li></ul><ul><li>2 unknown leaf categories</li></ul><p><strong></strong> </p><p><strong>Mercator4 v0.2 - Beta version</strong> </p><ul><li>26 functional root categories (BIN-01 .. BIN-26)</li></ul><ul><li>3744 leaf bin categories (including 1182 scaffold categories)</li></ul><ul><li>1 unknown root category (BIN-35)</li></ul><ul><li>2 unknown leaf categories</li></ul>Marie Bolger2021-10-04T15:25:55ZFrontPage 4.1Marie Bolgerhttp://plabipd.de:-1/portal/web/guest/wiki/-/wiki/34998/FrontPage2021-10-01T17:56:25Z2021-10-01T17:56:25Z<h4 id="section-FrontPage-Mercator4"> Mercator4 <a class="hashlink" href="#section-FrontPage-Mercator4">#</a></h4><p>Mercator is an automated high performance plant functional annotation and classification tool. It can be used to annotate plant fasta files and for downstream analysis in the MapMan application. </p><p><strong>Mapping files generated by Mercator4 can be used in the MapMan application, but the Pathway diagrams must start with X4 and correspond to the version of Mercator</strong>. </p><p>Users may still use old pathways (name does not start with X4), but these can only be used with mapping files generated from the older version of <a href="https://plabipd.de/portal/mercator-sequence-annotation">Mercator</a>. </p><p>If you have any further questions, you may contact b.usadel[at]fz-juelich.de </p><ul><li> See navigation tab <a href="https://www.plabipd.de/portal/web/guest/mer"><strong><em>about Mercator</em></strong></a> for details about Mercator4 online plant protein annotation tool</li></ul><p>If you find Mercator4 useful <strong></strong>please cite:- </p><p>Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B </p><p>MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. </p><p><a href="https://doi.org/10.1016/j.molp.2019.01.003">Mol Plant. 2019 Jun 3;12(6): 879-892</a> </p><p>If you use the older version of Mercator, please cite:- </p><p>Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B. </p><p>Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. </p><p><a href="https://doi.org/10.1111/pce.12231">Plant, Cell and Environment. Vol. 37, no. 5. 2014.</a> </p><ul><li><a href="">FAQ</a></li><li><a href="">Revision History</a></li></ul><p>Please evaluate this <a href="https://www.denbi.de/"><img src="https://www.plabipd.de/portal/documents/10181/0/deNBI_logo_normalized.png/c943c1f6-bfab-439a-aaff-aaa7443722d8?t=1479918831634" /></a> service! Let us know what you need and how we can improve; and give your <a href="https://www.surveymonkey.de/r/denbi-service?sc=gcbn&tool=plabipd">feedback </a> </p>Marie Bolger2021-10-01T17:56:25ZFAQ 1.1Marie Bolgerhttp://plabipd.de:-1/portal/web/guest/wiki/-/wiki/34998/FAQ2018-10-10T10:09:38Z2018-10-10T10:09:38Z<ul><li>Can I submit a fasta file containing both DNA and protein sequences?<br/><ul><li>No, this will result in an error. Fasta files submitted to Mercator4 must be exclusively DNA or Protein sequences.</li></ul></li><li>Very few of my sequences are assigned to functional bins. Why?<br/><ul><li>You should verify that that you have selected the correct sequence type (DNA or Protein) before submitting the mercator job. If you submit DNA sequences, but specify the 'Sequence type' as Protein, an error will be not be generated, but very few sequences are likely to be assigned to functional bins.</li><li>If you are sure that you have selected the correct sequence type, verify that you have submitted gene sequences (introns must be removed).</li><li>Mercator is designed for plants: If you submit sequences from non-plant organisms, the classification and annotation rate will likely be low.</li></ul></li><li>I get an error that my sequences are incompatible with Mercator - what can I do?<br/><ul><li>Mercator4 has been upgraded to accept a number of ambiguous protein sequences. However, there are still certain criteria which a sequence has to meet.</li><li>To validate your sequence for Mercator4, you can run your fasta file on the 'Mercator Fasta Validator' tool which will give a detailed report including the possibility to generate a 'Mercator valid' fasta file with the offending records removed.</li></ul></li><li>I get an Unknown Error/Internal Error/Server Error when running my job. What does this mean?<br/><ul><li>We try to handle every error scenario and provide a detailed description why the job failed. If you experience such an error, please send an email to plabipd@gmail.com with the 'JOB ID' (Starts with GFA-XXXXXXXX).</li></ul></li><li>I ran my sequences on Mercator4 six months ago, but now the version has changed. Can I run my sequences against an older version?<br/><ul><li>Yes. We provide a 'Legacy Mercator' tool which will allow users to run against older versions of Mercator4.</li></ul></li><li>My Job has been queued for hours. Is it really running?<br/><ul><li>This cluster is capable of running many jobs in parallel, but can still be overpowered if many users submit jobs simultaneously. If your job has been queued for hours, submitting the same jobs again will not speed up the process. If your job has not completed after 4 hours, then you should contact us at plabipd@gmail.com providing us with the 'JOB ID' .</li></ul></li><li>My browser crashed while running a job, and now I cannot access my job any more. What can I do?<br/><ul><li>As we do not require users to login to submit a job, the only way we have to track your job is using a 'browser session'. If your browser has crashed, then a new session is created and the link to your jobs is lost. However, if you entered a email address when you submitted the job, you will still be notified (along with a link to the results) when the job has finished. If you did not enter an email address, but have taken a note of the JOB ID, then you can email us at plabipd@gmail.com to get the results.</li></ul></li></ul>Marie Bolger2018-10-10T10:09:38Z