Link to this post | posted 16 Apr, 2019 15:19
dmonti	The term ribonuclease was used in the past and no longer appears on the official function list. Was there a particular reason for removing it from the list?

Link to this post | posted 01 Feb, 2019 19:23
dmonti	Yes - I just hesitated when I saw the new note associated with the function 'membrane protein' in the Official Function List at seaphages.org. It reads "at least two (2) transmembrane domains found using TMHMM." My group was assigning the function 'membrane protein' using the 'rules' outlined in the Bioinformatics Guide and which you re-iterated above. The clarification is helpful. Thank you!

Link to this post | posted 30 Jan, 2019 21:13

dmonti

Would it be possible to get greater clarification for the function assignment 'membrane protein?' The online bioinformatics guide states the following "a protein can be assigned the function "membrane protein" based on the results of the programs TMHMM and/or SOSUI. We use this assignment if we find two or more potential membrane domains predicted by one of the programs, or, a single membrane domain predicted with confidence by both programs." The official function list seems to require 2 confirmed transmembrane domains for the function 'membrane protein' to be called. Is it acceptable to assign the function membrane protein with only 1 TM confirmed by TMHMM and SOSUI? Thank you for any guidance!

Link to this post | posted 11 Sep, 2018 22:59

dmonti

Hi Deb and Chris - Thank you for the rapid replies. I tried the recommended fix and no luck. The 'Verify' button indicated all was ok but, unfortunately, the "Rebuild" button did not successfully restore the files or remove the error message. I tried to verify and rebuild all 3 of the files recommended in the post and in different orders to no avail. I also tried deleting all of the GenBank packages and it still would not even allow me access anything when I clicked "Submit to GenBank' from the Tools menu. Alas (with one small tear), I uninstalled DNA Master and re-installed again. I lost my GenBank packages but I had all of the files so I could re-create them again. Hope the BLOB doesn't strike anyone else! Best, Denise

Link to this post | posted 10 Sep, 2018 15:23

dmonti

DNAMaster recently updated on my PC and I am no longer able to open the 'Submit to GenBank' window. The version is 5.23.2, Build 2592, 26 June 2018. I am running with Admin privileges and can open a dnam5 and all looks and works fine. When I click on Tools - Submit to GenBank, I get the error message "BLOB has has been modified." Didn't have this problem last week. Any suggestions to 'unmodify' the BLOB? Best, Denise Edited 10 Sep, 2018 16:48

Link to this post | posted 02 Mar, 2016 22:12
dmonti	Hi Dan - The fastq file is rather large so I think it is going to take an overnight load to Dropbox. I'll let you know when I have it uploaded successfully. Thanks! Denise

Link to this post | posted 02 Mar, 2016 21:47

dmonti

HI Dan - My apologies for the delay. After your post, I wanted to go back and add in more reads to see if I perhaps missed the drop in coverage indicating a defined end. It took me a few days to get around to working in the sequence again. I did add in the reads and I see one spike in coverage, but it doesn't look like a terminal repeat. I would greatly appreciate a 'keener' pair of eyes. I will post the original Lamar.fastq file as well as the newly downsampled Lamar_100k.fastq file. Is there another file you need? I have a dnam5 file created from the Lamar_100k contig that I will also upload. Gene 121 is the terminase. Many thanks! Let me know if you want me to send anything else! Denise

Link to this post | posted 25 Feb, 2016 18:19

dmonti

Hi Dan - This is a phage called Lamar that is an Acinetobacter phage. Both Lamar and Beth are very interesting in that they form very distinct halos which we have not seen described for Acinetobacter phage. But the sequences for Beth and Lamar are very distinct; Lamar is about 30,000bp larger than Beth and no sequence similarity that we can see via a quick dot plot. I can send a dnam5 file if you wouldn't mind putting some expert eyes on the sequence. The terminase is gp121, there seems to be a chunk of structural genes around gp117-119 and again around gp88-92. I am just unsure where the 'logical' breakpoint would be. I may take Chris' suggestion and look in some of the other Acinetobacter baumannii phage to see if there is precedence for where to start the genome relative to the terminase. Other suggestions? Denise

Link to this post | posted 25 Feb, 2016 05:35

dmonti

Hi Lee - Thanks for the response. We are even struggling to find a tapemeasure gene but the good news is we finally did locate a terminase gene today! Unfortunately though, some questions remain. I know Welkin was using the terminase gene to determine a start position for a circularly permutated genome. The position of our terminase is at the end of a long string of forward genes with a few reverse genes sprinkled here and there. I am struggling to determine where I should assign position 1 in the genome. Should I 'ignore' the reverse genes for now and assign position 1 at the beginning of the forward genes, or take a different approach and assign position 1 at the short string of forward genes that immediately follows the first tiny reverse gene. Any advice is greatly appreciated! Denise

Link to this post | posted 24 Feb, 2016 21:12

dmonti

Hi Folks - We are attempting to create a final FASTA file for one of our recently sequenced phage and need to locate the terminase to know where to assign position 1 of the genome. After many BLAST searches and a few HHPred searches of nearly every protein with a typical terminase size, I am coming up empty-handed. Are there any other tricks or tips that you can share regarding locating the terminase? We have also tried running a dotplot comparison with other Acinetobacter phage and nothing seems to match. Many thanks for any assistance you can offer! Best, Denise