Link to this post | posted 12 Aug, 2022 16:07
afreise	Hi Debbie, Got it! I figured synteny was the reason the other pham members had been assigned that function. Thanks, Amanda

Link to this post | posted 11 Aug, 2022 18:53

afreise

Hello! I have a follow-up question about another potential small terminase gene, GalacticEye_Draft_6. I've attached a summary of the analysis I ran based on other forum posts on this topic. Key points below: Evidence FOR: Downstream gene is terminase, large subunit. (Synteny) A few other genes in this pham have called terminase, small subunit (all CS phages); they have e-value of 0 on PhagesDB BLAST. PCOILS appears to predict some coil-coil (I’m not sure if I’m interpreting this correctly DNABIND predicts DNA-binding function Evidence AGAINST: NO HHpred hits of significance for this gene when searching thru PECAAN (SCOPE, PDB, PFam). NO evidence of HTH-binding function 84Kb

Link to this post | posted 04 Aug, 2022 21:28
afreise	Chris, thank you so much for the info and your advice on false negatives. I decided to leave it as NKF based on that rationale. It's helpful to hear about your investigation process too. Thank you!

Link to this post | posted 04 Aug, 2022 01:36

afreise

On a similar topic - I am reviewing PumpkinSpice_33 in PECAAN (stop site 15,395). MLEHKLEEILEWLLILSLAVKENHWNLRGKEFFYLHEKLDELNDDITEYADTIAERARAREMYLAPKVAYEFSGESVSYTQAVNGIKSSLENLTMVLSGAIFNITDDLATQDVLIETKRGVDKWLWMFTESSR Several genes in the same pham, including cluster member MindFlayer_33, call DNA binding protein as the function (though Jay2Jay, mentioned in the previous post, ended up as NKF). It seems like there is some CDD evidence to support this. There is one CDD hit which mentions nonspecific DNA binding: cd01043 "DPS protein, ferritin-like diiron-binding domain." CDD hit stats: 32% identity 44% coverage 93% probability And another: COG0783 "DNA-binding ferritin-like protein" CDD hit stats: 25% identity. 41% coverage 93% probability Are these sufficient evidence to call DNA binding protein? Thanks, Amanda Edited 04 Aug, 2022 01:37

Link to this post | posted 14 Jul, 2022 19:31
afreise	Thanks, Debbie - I did try BLASTing a subset (the first five genes) and got the same issue.

Link to this post | posted 14 Jul, 2022 18:28
afreise	*One other note: We did all our annotations in PECAAN, which I think does re-BLAST automatically if a different start site is chosen. I then exported the annotation and used it to parse genes in the FASTA file in DNAM in preparation for the minimal file. With that in mind, do I need to do the re-BLAST within DNA Master?

Link to this post | posted 14 Jul, 2022 18:17

afreise

Hi all, I'm also running into issues with BLAST. My version of DNAM is 5.23.6, Build 2705, 14 October 2021.I did install the file that Dan shared above using his directions. When I tried to re-BLAST the entire genome last night, it did seem to send all the queries and read results, but I did get some errors like the following: Error (4) retrieving results for RID FA02Z622015 for feature 280 I'm also getting errors called "Error sending results to QBlast server" Unfortunately when I woke up and checked the results this morning, DNA master had completely crashed so I don't know if that BLAST search worked or not. I tried to BLAST a single gene, and it doesn't seem to be doing anything at all. The window has displayed "Sending BLAST request" for 5 minutes and no other updates are coming through. I also tried to blast a subset (the first 5) genes and I am getting the same "error retrieving results". Any thoughts on what I can try next? Thanks, Amanda Edited 14 Jul, 2022 18:49

Link to this post | posted 11 May, 2022 23:52

afreise

Hello! Please share with any interested colleagues, graduate students, or postdocs. – The Department of Microbiology, Immunology, and Molecular Genetics (MIMG) at UCLA is looking for two new full-time lecturers to welcome to our teaching team! Application: https://recruit.apo.ucla.edu/JPF07486 The new lecturers will join current faculty and staff in teaching an exciting curriculum to motivated and engaged MIMG undergraduate students. Classes to be taught may include, but are not limited to, General Microbiology, Microbiology for Nursing Majors, Research Immersion in Virology, Microbiology Lab for Pre-Professional School, Scientific Analysis and Communication, and more. At MIMG we are proud of our cutting-edge courses and focus on undergraduate research. Our lab classes are inquiry-based and encourage students to develop critical thinking skills as well as foundations in microbiology. We have collaborations with faculty on campus in multiple departments as well as off campus, including the HHMI-funded SEA-PHAGES program. Our teaching faculty work closely together and create a strong, supportive community in the department. We are seeking team players who are excited to get students engaged with microbiology and research. Please apply here by June 6 for priority consideration. The application will be open until filled: https://recruit.apo.ucla.edu/JPF07486 Please reach out to me with any questions! (afreise@ucla.edu)

Link to this post | posted 10 May, 2022 17:02

afreise

Hi Christian, I think I may be running into the same bug (?) when I try to compare multiple clusters. Right now I'm trying to compare between clusters CA, CB, CC and CE. when I run the following commands, 1. mysql -u root -p Actino_Draft -e "SELECT PhageID, PhamID FROM gene WHERE PhageID IN (SELECT PhageID FROM phage WHERE Cluster IN ('CA', 'CB', 'CC', 'CE' )) ORDER BY PhageID, Stop ASC;" -B -N >> ~/Rhodo_phams.tsv 2. phamclust ~/Rhodo_phams.tsv ~/Rhodo_gcs -m gcs I get multiple output text files, one of which has all the CA phages compared to each other, and the multiple other ones just have one phage each in them compared to itself. I tried running the upgrade command pip install –upgrade phamclust but it gave me the error: ERROR: Invalid requirement: '–upgrade' Can you advise re: the upgrade command? Should I be entering it after a specific other command? I've tried a couple ways. Best, Amanda

Link to this post | posted 29 Apr, 2022 21:34
afreise	In the Function Frequency box, I often see phams listed that are not the same pham as the gene I am looking at. Sometimes the functions are similar, but not always. It's a bit confusing because I don't want to rely on different phams for functional evidence. What is the rationale for including these different phams, and am I interpreting it incorrectly? Thanks! Amanda