Link to this post | posted 11 May, 2023 18:18

scaruso

Hello, I am at one of the schools that not only sends phage genomes to PITT for submission, but occassionally submits to GenBank directly when we work on different species. We do so by emailing the submission file in right from DNAM with the appropriate information. Recently I received a note that there is a format change (see below) and I now wonder if requires a change I am unsure how to make. If anyone can share any updates on this, I would be grateful. Thanks! Steve You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn. table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions. We will process this tbl2asn submission. DO NOT resubmit it. You will be contacted regarding its processing in a separate message, and you can complete any necessary changes to this submission as usual. However, for future submissions, we encourage you to use the newer command line program table2asn to generate the appropriate .sqn file for submission. Information about table2asn can be found at: https://www.ncbi.nlm.nih.gov/genbank/table2asn/ The values of a few arguments have changed compared to tbl2asn. In particular: Old New Purpose —————————————————————– - -help to get a summary of the command line arguments -p -indir to use all the .fsa files in the specified directory as input -r -outdir to deposit the output files in the specified directory -Z <file> -Z to run the discrepancy report -a r10k -gaps-min 10 to convert runs of 10 or more Ns to gaps of estimated size

Link to this post | posted 25 Mar, 2022 03:17

scaruso

Hello, There is certainly a history of that PHAM being called a holin: https://phagesdb.org/genes/Langerak_CDS_28/ TOPCONS shows it to have two TMDs and most of the internal tools agree, with the ones disagreeing showing one TMD. https://topcons.cbr.su.se/pred/result/rst_3pzb2qao/ HHPred doesn't show the TMDs, as you mention, but has a perfect PFAM hit to the holin: https://toolkit.tuebingen.mpg.de/jobs/Lang. PFAM isn't the best, but it's a full length hit. And it's been called in lots and lots of places: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=3UCM7VF0013. On one of ours, I would feel pretty comfortable with it. I hope that's helpful, Steve

Link to this post | posted 22 Mar, 2022 15:01
scaruso	Thank you! Steve

Link to this post | posted 21 Mar, 2022 14:14
scaruso	Good morning all, Has anyone noticed an issue with PECAAN running BLAST over the last week? I have checked the jobs table, and they haven't been changing. Is it down? Steve

Link to this post | posted 01 Feb, 2022 22:59

scaruso

DanRussell Hi Steve, There's a forum thread that talks about this error, but apparently the link to the fix isn't working anymore. https://seaphages.org/forums/topic/4436/ But this should be basically the same thing. Maybe try installing one of the Visual C++ packages here and giving it a shot? https://docs.microsoft.com/en-US/cpp/windows/latest-supported-vc-redist?view=msvc-170 –Dan Any chance you know how to deal with the error messages: An error occurred while attempting to initialize the Borland Database Engine (error #2108 ) and Queries table corrupt; reload from DNA Master FTP site? I have agreed to the latter. Tried uninstalling, reinstalling, reinitializing the database, etc. But DNAM simply doesn't work on the 'puter anymore. Steve Edited 01 Feb, 2022 22:59

Link to this post | posted 01 Feb, 2022 22:00
scaruso	Thank you, I will try it right away. Steve

Link to this post | posted 01 Feb, 2022 21:31

scaruso

Hello all, I have tried installing DNAM on a new Windows 11 machine in my teaching lab since it won't run on my old office computer anymore, and it installed. Once all the setting were updated, I tried BLASTING a gene and got: Could not load SSL library. This is very troubling since we start using DNAM in class on lab computers tomorrow. Any ideas from anyone? I am at a loss to get DNAM to work at UMBC. Steve

Link to this post | posted 04 Oct, 2021 20:02

scaruso

I have been unable to use DNA Master for the last few weeks. It may or may not be coincident with a Windows 10 update, I can't be sure, I'm afraid. But I am getting a "Error occurred while attempting to initialize the Borland database" message alternating with "Query table is corrupt." I have tried rebuilding the database and reinstalling DNAM, but same issue. Has anyone else had this issue? I am at a loss. I also need to provide the program to our DoIT soon for the spring, but I don't know what to give them, now, since the link from PITT is often non-functional. I would appreciate any guidance anyone can provide. Steve

Link to this post | posted 20 Sep, 2021 18:21
scaruso	Hello all, Any new news? DNAM suddenly failed on my machine. No changes made, just the databases up and quit. Can't re-initialize. I'm a little nervous for the Spring. Do we have a version to give to my DoIT? Steve

Link to this post | posted 30 Jun, 2021 19:59
scaruso	I am grateful. Steve