additional digests DMAC-48A

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chauser
Posts: 47
Joined: Wed Jan 31, 2007 3:34 pm

additional digests DMAC-48A

Post by chauser » Wed Mar 03, 2010 11:11 pm

Chris,

Are additional digests available for DMAC-48A other than those that came with the project?
We have a couple of frags present in in-silco absent in real that look real.

Chuck

cshaffer
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Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
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Post by cshaffer » Thu Mar 04, 2010 1:42 pm

The DMAC series does not have any extra digests.

The missing/extra bands can occur by the computer mis-calling the bands. We have software to look at the raw data (gel images) to see if there was a likely mis-call but its unix-only and complicated to install. The best thing to do is get in touch with Wilson email, he can help you with this analysis.

wleung
Posts: 182
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

additional digests DMAC-48A

Post by wleung » Wed Mar 10, 2010 4:01 pm

You can take a look at the static gel image through the "Digest Viewer" tool available through the GEP home page (Projects -> Digest Viewer). Once you navigate to the page, type in the name of the project (DMAC-48a) and then click the "Search" button. You will then see the static gel image with all four digests and the corresponding fragment sizes. The hash marks in the gel images correspond to bands that were called.

As Chris mentioned, the processed gel image data are available in a fpc database. The FPC software allows us to adjust the contrast of the gel image dynamically to determine if there are bands that are miscalled.

If you suspect that some of the bands are missing in the real digests, you can compare the total fragment sizes for all four of the digests. If the total fragment size of one of the digest is less than the other digests, then it is likely that there are bands that are missed by the band caller.

In this case, the total size of the digests for HindIII, EcoRI are about 46kb. The EcoRV digest has a total size of 57,259. However, this is likely caused by an incorrectly called doublet at 10984. If we subtract one of the 10984 band, the total size is about 46kb. The SacI digests has a total size of 45 kb, which suggests that there may be extra bands that were missed by the band caller.

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