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Recent Activity
All posts created by debbie
| Link to this post | posted 28 Feb, 2020 02:28 | |
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Greg, Here are my best answers: Is there a way to align the two DNA sequence files to determine where the nucleotides have been added or deleted? Yes! Use the align 2 sequences at ncbi's blastn. But my best guess is that there are 2 Ns at the end of the longer sequence. i would check there first. |
| Link to this post | posted 19 Feb, 2020 18:05 | |
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Just looked at 2 cluster AO2 phages, JKerns and StevieBAY. StevieBAY's gene 28 is an endolysin. It possesses all of domains we expect to see in an endolysin. Gene 64 codes for the CHAP endopeptidase domain of LysK (a Staphylococcus phage lysin gene). It is reported out as an endolysin also. We won't call either of them lysin A (Reserved only for mycobacteriophages for now, unless the phage genomes contains a lysin A and a lysin B. |
Posted in: Cluster AO Annotation TIps → LysinA and endolysin
| Link to this post | posted 12 Feb, 2020 18:45 | |
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Deb, The file (not the program) is likely corrupted. Follow these directions in the Bioinformatics Guide. https://seaphagesbioinformatics.helpdocsonline.com/article-104 It is tedious, so be careful as you do this. If it doesn't work, send me the file. Good luck! debbie |
Posted in: DNA Master → TbQueries
| Link to this post | posted 05 Feb, 2020 21:09 | |
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Excellent idea! Thanks Chris! |
Posted in: Starterator → Database Version for starterator
| Link to this post | posted 02 Feb, 2020 20:00 | |
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Amy, If send me the file, I will try to fix it. debbie |
| Link to this post | posted 30 Jan, 2020 21:16 | |
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Gene 73 of phage Krampus is best labeled as a RuvC-like resolvase. Resolvase is too general of term to use. (Determined in a conversation with G. Hatfull. |
Posted in: Cluster EF Annotation Tips → RuvC-like resolvase
| Link to this post | posted 24 Jan, 2020 20:17 | |
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In calling the immunity repressor of a phage JF2 (gp71), we came across a peculiar finding. It seems that the immunity repressor's open reading frame has less coding potential than another open reading frame in that area. Don't be fooled! JF2's immunity repressor shows hits in HHPred to the HTH DNA binding site (N-terminus). Read Pope, et al 2011a for info about Bxz2's broken repressor. However, our gene doesn't match that N terminus either. Many (did I say many?) phages have miscalled the open reading frame as the immunity repressor. Be careful. We will fix as soon as we can. debbie |
Posted in: Cluster A Annotation Tips → Cluster A3 Immunity Repressor?
| Link to this post | posted 23 Jan, 2020 17:01 | |
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Greg, It is 11:59am on January 23 and I was able to update with no problem. The latest update is version 5.23.3, Build2640, 22 January 2020. Are you still having problems with the update? |
Posted in: DNA Master → DNA Master Failing to Update - 01.23.2020
| Link to this post | posted 21 Jan, 2020 19:24 | |
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Hi Ann, the answer is in Setting Preferences in the on-line Bioinformatics Guide. It is item #2 (click the box and enter "Hatfull" as the password), but check the other preferences while you are there. Thanks, debbie |
| Link to this post | posted 21 Jan, 2020 15:27 | |
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Nancy, Hi. Your preferences are not set correctly. The NCBI servers are not available to us anymore. Check Setting Preferences in the on-line Bioinformatics Guide, #2. Click the box and the password needed is Hatfull. You may want to check all of the preference settings while you are at it. debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later