More NRPS slides

diff --git a/antismash_lca2011.html b/antismash_lca2011.html
index 20407410396d3529c8f50b8f2cf20aa698ea2a35..d4e1825760c2ed6935df2abcf8a2e9ad770de978 100644 (file)
--- a/antismash_lca2011.html
+++ b/antismash_lca2011.html
@@ -264,6 +264,23 @@
 
   <section class="slide" id="antismash-clusterblast">
   <h2>Cluster BLAST</h2>
+  <img src="clusterblast10_all.svg">
+  </section>
+
+  <section class="slide" id="antismash-nrps-cluster">
+  <h2>NRPS Cluster</h2>
+  <img src="nrps_cluster.svg">
+  <div class="slide" id="antismash-nrps-modules">
+    <h2>NRPS Modules</h2>
+    <img src="nrps_modules.svg">
+  </div>
+  </section>
+
+  <section class="slide" id="antismash-svm">
+  <h2>Support Vector Machines</h2>
+  <div id="svm-canvas"><img src='classification-untrained.png' height="500"></div>
+  <div class="slide" id="antismash-svm-trained"></div>
+  <div class="slide" id="antismash-svm-new"></div>
   </section>
 
   <section class="slide" id="antismash-smcogs">

diff --git a/antismash_talk.js b/antismash_talk.js
index 848e3ec7919296a5d5d5aa9141d54cc01a3bdddb..d64df163c35922bd733d7a9485ab5c72ec97d970 100644 (file)
--- a/antismash_talk.js
+++ b/antismash_talk.js
@@ -46,6 +46,15 @@ $(function() {
     case "antismash-find-orfs-all":
       $("#orf-canvas").html("<img src='sequence_annotated.svg'>");
       break;
+    case "antismash-svm":
+      $("#svm-canvas").html("<img src='classification-untrained.png' height='500'>");
+      break;
+    case "antismash-svm-trained":
+      $("#svm-canvas").html("<img src='classification.png' height='500'>");
+      break;
+    case "antismash-svm-new":
+      $("#svm-canvas").html("<img src='classification-new.png' height='500'>");
+      break;
     }
   });
 });

diff --git a/cdma_cluster.svg b/cdma_cluster.svg
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index 0000000..87d99fb
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diff --git a/script.txt b/script.txt
index de9e7db6f1b02d52676282ca00921c50952a84e4..765b07c4a16c0d62d16664e950ff55eb14c4890b 100644 (file)
--- a/script.txt
+++ b/script.txt
@@ -333,11 +333,23 @@ In this visualization, similar colors mean the comparison algorithm found
 similarities between these genes. The actual comparison again happens on the
 amino acid sequences, of course.
 
-In case we identify an NRPS cluster, there is an additional step we can take to
+In case we identify an NRPS cluster, there are some additional steps we can take to
 do an even better job at predicting the product. As you will recall, NRPSes are
 factory line enzymes with very specific modules. By analyzing the modules, we
 get a pretty good clue on what substances the modules add to the final product,
-and what other possible modifications might happen.
+and what other possible modifications might happen. In order to perform this
+analysis, we're actually implementing three different approaches that we build
+a consensus annotation from. Two are profile-based approaches again that work
+similar to the initial cluster identification.
+
+The third is a more elaborate method that allows different levels of
+predictions on the NRPS product. The program we use is called NRPSPredictor2,
+and was developed at the University of Tübingen. NRPSPredictor is using a
+support vector machine to predict the module-specific substance. If the module
+isn't close enough to already known modules, which unfortunately happens once
+in a while, NRPSPredictor can fall back to predicting more general properties
+of the module's substance. For example, the prediction could be "it's one of
+the charged amino acids".
 
 FastTree/smCoGs