Link to this post | posted 20 Feb, 2021 00:03
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Link to this post | posted 20 Feb, 2021 00:02
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Link to this post | posted 19 Feb, 2021 23:39

nietof

Hey Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Link to this post | posted 19 Feb, 2021 23:38

nietof

Hey Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Link to this post | posted 05 Jan, 2021 15:07
nietof	Debbie Thank you, I will try that, and Happy New Year!!! F

Link to this post | posted 05 Jan, 2021 12:38

nietof

I am running DMA Master in windows 10. Set it up all preferences according to latest instructions. I am able to autoannotate my genome. I ran the BLAST all genes overnight and it doesn't complete. DNA Master becomes unresponsive and the only way to get out is by ending it using task manager. This is the first time I am running DNA Master in windows 10 and it is a brand new laptop. Thank you Fernando

Link to this post | posted 09 May, 2020 20:52
nietof	Hi Dan THank you. Trust all is well with you the UPitt folks and your families. Best F

Link to this post | posted 09 May, 2020 16:58
nietof	Hi The entry for Temperate shows either true or false, but in some instances the entry for this column is none. Is none the same as false? thank you Fernando

Link to this post | posted 09 Mar, 2020 17:58
nietof	Hi What is the best way for downloading fasta files for a selected group of phages to build phylogenetic trees? I downloaded the complete fasta file from phagesdb and then I searched the sequences using the phage names, but it takes forever for large clusters like A1. Thank you Fernando

Link to this post | posted 21 Jan, 2020 16:00
nietof	Hi Dan I am using a school laptop from home, the laptop was initially set up by our IT. I am working using an administrator account. I found a post on DNA Master and Windows 10 from Welkin dealing with the Windows 10 UAC. I follow her instructions to add DNA Master as a trusted application in windows 10. I reinstalled DNA Master. Let's see how long it works. Thank you F