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Commit 81b3a5a9 authored by Davide Lagoa's avatar Davide Lagoa
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readme instructions updated

parent 68372976
......@@ -10,4 +10,37 @@ and used to reach optimal values for the parameters.
SamPler was implemented as a new plugin for merlin’s current version. merlin is freely available at http://www.merlin-sysbio.org/.
Instructions to install SamPler:
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Instructions to install SamPler:
1. Unzip merlin-sampler.zip file
2. Paste merlin-sampler folder inside plugins_bin
3. Start merlin
4. Open a workspace having already enzyme annotation results.
Note: The loaded workspace should have enzyme annotation results in merlin's enzymes annotation view after performing the similarity searches (and only this step).
For more details, please consult https://merlin-sysbio.org
5. In the workspace's clipboard, go to annotation -> enzymes (let merlin's enzymes annotation view open)
6. In the upper menu, go to annotation -> enzymes -> SamPler
7. Select the respective workspace
8. To proceed, SamPler will discard any previously set parameters and annotations for the blast database selected in merlin's enzymes annotation view
9. SamPler automatically selects a random sample of genes to be annotated.
The sample size corresponds to 5% (by default) of all candidate genes to encode an enzyme
10. To generate a new sample of genes of a different size, enter the new sample size (%) and select new sample.
SamPler will create a new random sample of genes corresponding to the selected size.
11. Perform the enzyme's annotation (select the correct EC number) within the sample selection window according to a manual curation workflow of your choice.
12. After annotating each gene in the sample selection window select "find best parameters".
13. SamPler will calculate the curation ratio score for each alpha value and its most adequate and strict thresholds.
The alpha value having the best curation ratio score is selected by default.
14. The results' view allow one to lower the precision and negative predictive value for the upper and lower thresholds, respectively.
Note: By lowering both precision and negative predictive value metrics for the upper and lower thresholds,
one is considering the automatic annotation of false positives and rejection of false negatives, respectively.
15. Select the alpha value having the best curation ratio score for the precision and negative predictive value confidence levels of your choice.
16. Click "apply" to re-calculate merlin's internal scoring algorithm for the enzymes annotation according to the alpha value selected.
17. The selected alpha value and corresponding thresholds are updated in merlin's enzyme annotation view
18. According to SamPler, genes having an annotation score higher than the upper threshold should be automatically accepted,
while genes having an annotation score lower than the lower threshold should be automatically rejected.
The enzymatic annotation of the genes with annotation score in between should be manually revised.
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Manifest-Version: 1.0
Built-By: BioSystems
Build-Jdk: 1.8.0_201
Created-By: Maven Integration for Eclipse
#Generated by Maven Integration for Eclipse
#Wed Jul 03 15:04:58 BST 2019
version=0.0.1-SNAPSHOT
groupId=pt.uminho.ceb.biosystems.merlin
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m2e.projectLocation=C\:\\Users\\BioSystems\\merlin3\\merlin-sampler
artifactId=merlin-sampler
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<artifactId>merlin</artifactId>
<version>3.9.4</version>
</dependency>
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