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Glitch in phagesDB GeneMark? Reverse frames being flipped!
| Link to this post | posted 26 Jan, 2024 02:19 | |
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As of Jan 25, 2024, whereas the forward frames are Okay, we have noticed a mismatch between the reverse frames in DNA Master and those of GeneMark outputs. We have noticed that that coding potential (CP) for DNA Master frame -1 is in frame -2; plots/data for frame -2 is in the -1 frame, and plots for frame -3 is in the -2 frame of the GeneMark_S, GeneMark_smeg, & GeneMark_TB plots obtained from phagesDB. Is there a glitch or are we missing something? See attached. Thanks! Fred |
437Kb| Link to this post | posted 26 Jan, 2024 14:51 | |
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Fred - my understanding is that each program determines how to label the different frames independently, so there is no "standard" for which is going to be -1, etc. You need to determine which aligns with which each time you compare the data from two different programs to make sure you are comparing apples to apples. Lee |
| Link to this post | posted 30 Jan, 2024 19:30 | |
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Thank you, Lee. Indeed, we pointed out the differences to our students and instructed them on what to do, though some still get confused by the mismatches. Since the forward frames in DNA Master perfectly match with the forward frames in the GeneMark coding potential outputs, we were just hoping that there was some way to twitch the GeneMark software for the reverse frames to match those in DNA Master as well. For now, we will just keep pointing out this difference between DNA Master frames and the GeneMark outputs with regard to the reverse frames. Fred |