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Recent Activity
Tricky gaps
| Link to this post | posted 18 Mar, 2023 19:58 | |
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I am exploring two gaps in Gusanita's ORF assignment by DNA Master and am having some trouble deciding if they are good to call or not. 1) Thoughts on deleting called gene, forward, 29241-29357 as it doesn't have good BLAST data and no other related phage have a forward gene in the middle of this reverse stretch. Possible new genes: 2) 29270 start, 28890 stop, reverse orientation, has a BLAST match, but not good HHPred data. This still leaves a gap here, but I don't see any other good options and no related phage give strong comparison in this area. 3) 34296 start, 34397 stop, -4 overlap, BLAST matches look good |
| Link to this post | posted 19 Mar, 2023 23:05 | |
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Using the phamerator numbers I would likely not call either 39 or 40. 34296 - 34397 has enough (though slight) coding potential for me to consider calling this one. No Other FF has this sequence. Note that this genome has 2 tRNAs, make sure there is not any overlap between genes/tRNAs. |
| Link to this post | posted 20 Mar, 2023 01:32 | |
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Thank you! That makes sense all around.debbie |