Difference between revisions of "Using Apes (A Plasmid Editor)"
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| + | ==Download ApE (A plasmid Editor)== | ||
| + | # Go to the web site to [http://www.biology.utah.edu/jorgensen/wayned/ape/ download the latest Windows or Mac version]. | ||
| + | # You will want to use a Feature search or align two sequences to verify your sequencing results. | ||
| + | # Open the .seq file from your sequence service provider. | ||
| + | # Delete any N's from the first and last parts, but leave "internal" Ns in place. | ||
| + | # It is helpful to identify the BioBrick ends first, so you can see where you are. | ||
| + | # Some times the sequencing did not work for technical reasons. | ||
| + | # You can confirm any Ns by looking at the chromatogram. | ||
| + | |||
==Quickly View Features of Sequence== | ==Quickly View Features of Sequence== | ||
1. Open the .seq file<br> | 1. Open the .seq file<br> | ||
| − | 2. Download [http://www.bio.davidson.edu/projects/GCAT/Synthetic/iGEMfeatures this] | + | 2. Download [http://www.bio.davidson.edu/projects/GCAT/Synthetic/iGEMfeatures this file], called iGEMfeatures<br> |
3. In the features menu on the toolbar select "Open Feature Library"<br> | 3. In the features menu on the toolbar select "Open Feature Library"<br> | ||
4. Select the file you downloaded in step 3<br> | 4. Select the file you downloaded in step 3<br> | ||
| Line 10: | Line 19: | ||
2. Click on the "New" button<br> | 2. Click on the "New" button<br> | ||
3. In the top field type the label of the feature you are adding<br> | 3. In the top field type the label of the feature you are adding<br> | ||
| − | In the bottom field type the sequence of the feature you are adding<br> | + | 4. In the bottom field type the sequence of the feature you are adding<br> |
| − | + | 5. Highlight the sequence and click the "Uppercase" button<br> | |
| − | + | 6. Choose the appropriate feature type and the appropriate color label<br> | |
| − | + | '''DO NOT FORGET TO SAVE CHANGES''' If you wish to add these features to the standard features file, be sure to update the file this page links to.<br> | |
| + | 7. This [http://gcat.davidson.edu/GcatWiki/images/3/3b/Ape_protocol.pdf PDF file] tells you how to align two sequences and was written by Dr. Heyer. | ||
Latest revision as of 13:51, 8 August 2012
Download ApE (A plasmid Editor)
- Go to the web site to download the latest Windows or Mac version.
- You will want to use a Feature search or align two sequences to verify your sequencing results.
- Open the .seq file from your sequence service provider.
- Delete any N's from the first and last parts, but leave "internal" Ns in place.
- It is helpful to identify the BioBrick ends first, so you can see where you are.
- Some times the sequencing did not work for technical reasons.
- You can confirm any Ns by looking at the chromatogram.
Quickly View Features of Sequence
1. Open the .seq file
2. Download this file, called iGEMfeatures
3. In the features menu on the toolbar select "Open Feature Library"
4. Select the file you downloaded in step 3
5. In the features menu on the toolbar select "Annotate Features Using Library" OR press ⌘K
Add Features
1. In the features menu on the toolbar select "Edit Feature Library"
2. Click on the "New" button
3. In the top field type the label of the feature you are adding
4. In the bottom field type the sequence of the feature you are adding
5. Highlight the sequence and click the "Uppercase" button
6. Choose the appropriate feature type and the appropriate color label
DO NOT FORGET TO SAVE CHANGES If you wish to add these features to the standard features file, be sure to update the file this page links to.
7. This PDF file tells you how to align two sequences and was written by Dr. Heyer.
