I am doing the analysis on the T-RFLP to study the microbial diversity. But the records are 10,000 to 20,000 or more for each digesting product. It is very hard to check them one by one to make a microbe list.
Any good idea? Any suggestions? Thank you very much.
How many restriction digests do you have? The list narrows down pretty quickly if you look for species common to two fragment lengths and you can often be fairly confident if you use three restriction enzymes. I use an excel spreadsheet with a list of bacteria and their fragment sizes with a number of enzymes, so I can filter by fragment size for each of the enzymes that I am using. Hope this helps.
Attached is a file that I have for bacterial 16S, based on 27F and 785R primers. I download the relevant data from the MICA site ( http://mica.ibest.uidaho.edu/. ) in March of 2013, for the enzymes of interest and then filter by the fragment sizes that I have. In the file I used BstUI 110, MspI 65 and HaeIII 225 as examples. Let me know if this helps.
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