Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
Debbie Jacobs-Sera posted in Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701
Viknesh Sivanathan posted in Top Agar contamination
Debbie Jacobs-Sera posted in Phage Enzyme Tools - PET2.0 - Down?
All posts created by afreise
Link to this post | posted 04 Aug, 2022 21:28 | |
---|---|
|
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! |
Posted in: Functional Annotation → DNA-binding ferritin-like protein
Link to this post | posted 04 Aug, 2022 01:36 | |
---|---|
|
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 |
Posted in: Functional Annotation → DNA-binding ferritin-like protein
Link to this post | posted 14 Jul, 2022 19:31 | |
---|---|
|
Thanks, Debbie - I did try BLASTing a subset (the first five genes) and got the same issue. |
Posted in: DNA Master → DNAMaster BLAST failure
Link to this post | posted 14 Jul, 2022 18:28 | |
---|---|
|
*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? |
Posted in: DNA Master → DNAMaster BLAST failure
Link to this post | posted 14 Jul, 2022 18:17 | |
---|---|
|
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 |
Posted in: DNA Master → DNAMaster BLAST failure
Link to this post | posted 11 May, 2022 23:52 | |
---|---|
|
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) |
Posted in: General Message Board → Two lecturer positions at UCLA
Link to this post | posted 10 May, 2022 17:02 | |
---|---|
|
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 |
Posted in: Bioinformatic Tools and Analyses → Difficulty pulling large-scale data for batch GCS analysis using Pope/Mavrich 2017 scripts
Link to this post | posted 29 Apr, 2022 21:34 | |
---|---|
|
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 |
Posted in: PECAAN → PhagesDB Function Frequency data
Link to this post | posted 09 Mar, 2022 17:50 | |
---|---|
|
Oh, I just realized this data pull does include draft genomes - so my first question is answered. |
Posted in: Bioinformatic Tools and Analyses → Difficulty pulling large-scale data for batch GCS analysis using Pope/Mavrich 2017 scripts
Link to this post | posted 09 Mar, 2022 17:32 | |
---|---|
|
WOW - thank you SO MUCH, Christian! It worked perfectly! Definitely easier than what I was attempting. A couple more questions, if/when you have a moment - -Is there a way to do the same analysis but include draft genomes? I want to do a preliminary analysis including drafts just to see where some of the newer AZ phages fall that haven't been manually annotated yet (not for publication, but just out of curiosity) -If I wanted to compare phages from multiple clusters, is that possible using an adjustment to the above script? For example, we are interested in including singleton phage BaileyBlu to the AZ phages, and/or other clusters such as EH. |