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Jeremy Garza posted in Phage Staining - Uranyl Acetate
Debbie Jacobs-Sera posted in Help with Annotating Direct Terminal Repeats
Marie Fogarty posted in Help with Annotating Direct Terminal Repeats
cdshaffer posted in Help with Annotating Direct Terminal Repeats
Marie Fogarty posted in Help with Annotating Direct Terminal Repeats
Tail Assembly Chaperone
| Link to this post | posted 07 Feb, 2024 07:04 | |
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hi We are annotating phage Aikyam. We noted that phages in this cluster with the same TAC pham, phage Isolde, for example, call the programmed frameshift using a slippery sequence CCCTTTTT (a PF to PF -1 slip). CCCTTTTT doesn't appear on any list of validated slippery sequences that I could find, so I wasn't sure why this site has been called. It certainly works as a slippery sequence, but is there any evidence to support this call? Other AY phages, like EvePickles, use CCCAAAAA (PK to PK; a different Pham), which does appear on Sup Table 1 from Xu et al. thanks Adam |
| Link to this post | posted 07 Feb, 2024 12:44 | |
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Adam, In the paper referred to the Bioinformatics Guide, the TAC 'template' is X_XX.Y_YY.Z. You have not provided enough information for me to look quickly, but check the guide to interpret the '_ 'and '.'s If your CCCTTTT lines up correctly for a -1 Frameshift, you have a canonical programmed ribosomal slippage. You also used an abbreviation 'PF' that i don't recognize. debbie |
| Link to this post | posted 07 Feb, 2024 13:04 | |
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Hi Debbie Ok, this was a misunderstanding on my part. I thought we needed to identify a slippery sequence similar to those that have been defined previously (i.e. on the table). CCCTTTTT definitely works as an XXXYYYZ sequence, and is in the correct position for a -1 frameshift. PF to PF referred to the slip as coding proline-phenylalanine to proline-phenylalanine. thanks Adam |