Link to this post | posted 20 Dec, 2023 22:16
rlb6	Has "ribosome modulation factor" been given any consideration as an official function? Belphegor gp13 (10420-10245)MIPRDQQPMPTPAEAIEAYKAGQVSRPGAGNPYAGRRVLGSVWALGNREAQRDAYTEFRRREAERRE 68AA, same pham as Fitzgerald. Beckie Bortz 52Kb

Link to this post | posted 14 Jun, 2021 20:29

rlb6

Regardless of whether I get the program from the FTP server or from the dropbox link, the installation of DNA Master is creating errors. Once I install and update, I get an "error creating fields", the program tries to "update helpers", and ends with "FTP failures". I enlisted help from Kristen and the same errors were obtained with a new installation on her machine. She tried turning off firewalls but this did not resolve the issue. DNA Master seems to essentially be working in this state but can't access data outside the program such as Blast or to pull in genomes for comparison. I am unaware what else may be affected. The Bitvise SSH client may be a solution to pull in all of the files correctly, but I am not savvy enough to know how to make it work. Any help is appreciated! I hope this info helps to trouble-shoot this error and generate a reliable fix before a large number of students require it. Beckie Bortz

Link to this post | posted 03 Jun, 2021 20:38
rlb6	Thanks Chris, I did miss that step having more commonly worked on pc. I was able to install windows and then DNA Master. Unfortunately, I still don't have an error free copy of DNA Master as I'd hoped. Beckie Bortz

Link to this post | posted 03 Jun, 2021 17:27

rlb6

I successfully used the steps from howtogeek above on my pc but I'm still getting a lot of error messages from DNA Master (see post under DNAMaster>>key violation). So … I reinstalled the virtual machine on my Mac and I've gotten as far as saving dnamaster.exe to the VM desktop but it won't install and states "an error occurred while loading the archive". See attached screenshot. Any thoughts about how I can get some error free version of DNA Master up and running? Beckie Bortz 1.29Mb

Link to this post | posted 26 May, 2021 16:43
rlb6	No change after restart. Still key violation error, "recent" files still missing, no msg that it can't find recentfile DB, no prompt for FTP. Beckie Bortz

Link to this post | posted 26 May, 2021 16:28

rlb6

I found the files but the problem is not resolved. (In Applications, right click on DNAMaster icon and select "show package contents". Click on "contents" then "resouurces" then "wineprefix" folder then "drive_c" then "program files" then "DNAMaster" then "DMDB".) I moved all "recent" files to a new folder and deleted them from the DMDB folder and restarted DNA Master. DNA master can open an archived file, but it is still giving the same "key violation" error and I do not see that the "recent" files have been restored nor am I getting popup table with the prompt to download from FTP. I'm going to try restarting my machine. Beckie Bortz

Link to this post | posted 26 May, 2021 15:50
rlb6	How does this advice apply to a mac running wine? I am getting the "key violation" error. Can I still produce GenBank and Phamerator files for submission with this error? Beckie Bortz

Link to this post | posted 21 May, 2021 17:43

rlb6

There is no appropriate official function for Gordonia phage Floral_39. There are, however, lots of hits for a SecB-like export protein or translocase. "The Escherichia coli soluble protein SecB is involved in the export of periplasmic and outer membrane proteins." Kumamoto CA. SecB protein: a cytosolic export factor that associates with nascent exported proteins. J Bioenerg Biomembr. 1990 Jun;22(3):337-51. doi: 10.1007/BF00763171. PMID: 2202722. Thoughts about this function? MSKKMSLAEGREAMVRVLQEIQGLKAVRASRIECEALRPLPDSVEEAALVTDVKVSFHASPPYLATFVLYRVCATWGEADEFTDVAEEDQAWRITLEFCADWEVSADAELASEDLRCFAVSQGVMTCHPYARETIQSASVRMGYPPATLDIIRNPLIGDGEIEFED Beckie Bortz 353Kb

Link to this post | posted 04 May, 2021 16:28

rlb6

Hi I'm looking for the best function assignment for a Gordonia gene LonelyBoi_31. This gene has strong hhpred and blast hits to acyltransferase and SGNH domains. Many transmembrane helices are also predicted. I don't see any appropriate function on the Official function list This is the amino acid sequence starting at nucleotide 29456 which seems to align best with the start of top hits: LRLDIQGLRAVAVILVILDHLFEWPKAGFIGVDVFFVISGFVITAGLQRGYGRTGTISFGDFYRKRARRI IPASTLVLVATCAAAAYAFYSSRFHETLIDAVWAFFFASNWRFAFQGTNYLTAEGPVSPLQHYWSLGIEE QFYVVWPLLMLGVFTLAASRGLHAHSERIAAAAIGLVIAVSFSWAMIQTATHAEFAYFSTFTRVWELGIG AMLALLAVEWKKIPDAARPFLAWVGLLGILVSAFIVSSESGFPAPWAALPVLATALVIAAGTGGERKHLY PLTNPVASYIGDISYSLYLWHFPVIVILAAMMPSGWRYHFLCLALMSILSVLSYHILEDPVRKSTWLEPK AVREDRRRLRRGASTTTLADSVGSAKWKIISLTAVLLVALAVVADGRGSDMSSVPDFTAAGQVSDNGAPT SPLQAGLVEGVEATKWPANLSPSLEELGDISFPTADANGCAPATPRGRDCTIAGVDPSRLAVVVGDSISV AWLPAIRAALEPKGWTVAALPYIGCPFVDGATENADATVVRTCPAHKQEVVDIINRAKPALVIGSSTNNI RSARGESPENGARALSDQVAKIDAAAGRYVQLSPPPSGDNPQECATRFSSPRECLGGLPSNYTASVEAQK AVMAGPGRQFVDTSDWFCTPEGDCPILNGSTLIRRDTSHITPQYAKVIAPQLASALLTTG Beckie Bortz 82Kb

Link to this post | posted 15 Apr, 2020 14:55

rlb6

FYI – The fix that Dan uses below recently (April 2020) worked for me as well. Thanks, Dan! –Beckie DanRussell Hi Katie, I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked. https://www.microsoft.com/en-us/download/details.aspx?id=5555 Hopefully that helps, –Dan Beckie Bortz Edited 15 Apr, 2020 14:56