Difference between revisions of "APe Sequence Analysis"
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# Download the free [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE software] if you want it on your own computer. All college-owned computers already have ApE installed so you can use those computers if you prefer. This tool is used by researchers all over the world. | # Download the free [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE software] if you want it on your own computer. All college-owned computers already have ApE installed so you can use those computers if you prefer. This tool is used by researchers all over the world. | ||
# Access your sequence files. Click once on a file with the .seq suffix. For Macintosh computers, hold down the command button and type i. A window will open. About halfway down the window under the heading "Open With", choose ApE as the application. Then click on the "Change All" button so that all .seq files will automatically open with ApE. | # Access your sequence files. Click once on a file with the .seq suffix. For Macintosh computers, hold down the command button and type i. A window will open. About halfway down the window under the heading "Open With", choose ApE as the application. Then click on the "Change All" button so that all .seq files will automatically open with ApE. | ||
| − | # Repeat step 2 above but use | + | # Repeat step 2 above but use one of your .ab1 file instead of .seq file. |
| − | # Download the [http://www.bio.davidson.edu/people/macampbell/113/weekly_Labs/plasmids.zip 4 receiving plasmids] and | + | # Download the [http://www.bio.davidson.edu/people/macampbell/113/weekly_Labs/plasmids.zip 4 receiving plasmids] and identify which plasmid you used. Open the correct .seq that was your receiving plasmid. |
# Open the appropriate .seq file for your eXperimental samples. | # Open the appropriate .seq file for your eXperimental samples. | ||
| + | # When open your .seq files, you will see some N bases. The software inserts an N whenever it cannot tell for sure which base should go there. The software that “calls” each base uses three criteria: phred score of quality; width of the peak; and spacing between peaks. Phred scores can be seen as the light bar graphs behind the colored lines. Good scores result in a bar graph about half way up the sequence box. Each base is associated with a different color line. | ||
| + | # Under the “Tools” menu, choose “Align Sequences…”. Choose your receiving plasmid.seq as the reference, using the drop down menu. In the “Align to Windows” field, select any comparison .seq files by clicking on the file names. Click on the button “Show Alignment Parameters and set them as shown. <br> | ||
| + | <center> | ||
| + | [[File:aligning.png]] | ||
| + | </center> | ||
| + | |||
| + | This will cause your sequence to not be split into small fragments. Click OK. | ||
Revision as of 16:04, 19 July 2017
ApE Software for DNA Sequence Analysis
- Download the free ApE software if you want it on your own computer. All college-owned computers already have ApE installed so you can use those computers if you prefer. This tool is used by researchers all over the world.
- Access your sequence files. Click once on a file with the .seq suffix. For Macintosh computers, hold down the command button and type i. A window will open. About halfway down the window under the heading "Open With", choose ApE as the application. Then click on the "Change All" button so that all .seq files will automatically open with ApE.
- Repeat step 2 above but use one of your .ab1 file instead of .seq file.
- Download the 4 receiving plasmids and identify which plasmid you used. Open the correct .seq that was your receiving plasmid.
- Open the appropriate .seq file for your eXperimental samples.
- When open your .seq files, you will see some N bases. The software inserts an N whenever it cannot tell for sure which base should go there. The software that “calls” each base uses three criteria: phred score of quality; width of the peak; and spacing between peaks. Phred scores can be seen as the light bar graphs behind the colored lines. Good scores result in a bar graph about half way up the sequence box. Each base is associated with a different color line.
- Under the “Tools” menu, choose “Align Sequences…”. Choose your receiving plasmid.seq as the reference, using the drop down menu. In the “Align to Windows” field, select any comparison .seq files by clicking on the file names. Click on the button “Show Alignment Parameters and set them as shown.
This will cause your sequence to not be split into small fragments. Click OK.
