Link to this post | posted 03 Jun, 2023 18:34

edgingtonn1

There is a Pham (which includes London_gp47) which has a group of proteins that have a good E-value on CDD, HHPRED, and structural predictions in AlphaFold, however: • These are usually part of a multi-gene system. What is the function of this gene by itself? • What is its function in phage multiplication? • This domain is in the ACT domain family, which is found in many different proteins with various functions and ligands. • The attached file has some of the evidence and predictions. Recommendation (from Karen K. and the SMART team): Keep as hypothetical protein for now. 8 Members of Pham 7014 as of 2023-06-03: Asa16_47 Ascela_50 Elezi_47 Eraser_47 Iter_50 London_47 Niobe_47 Nitro_Draft_51 Edited 06 Jun, 2023 14:48 2.70Mb

Link to this post | posted 02 Mar, 2023 18:09
edgingtonn1	Hi Christian, It hits the same biolib server on the CMD, but I was hoping that submitting them slowly overnight with a script might work, even if it was taking 5-10 minutes or longer per sequence. Instead, it just times-out, & kills the job. It looks like creating an account is the way to go – Thanks Chris! -Nick SCSU, New Haven CT

Link to this post | posted 01 Mar, 2023 19:26
edgingtonn1	DeepTMHHH keeps timing out (all day) both at the website (for my students and myself), and on the command line… Is it just me? -Nick SCSU, New Haven CT

Link to this post | posted 01 Aug, 2022 18:50
edgingtonn1	Thanks Debbie! I thought maybe I had missed a new directive. We have been following the guidance that if there is a single predicted TMD, then it must be called by at least two different TMD prediction programs. Best, -Nick

Link to this post | posted 01 Aug, 2022 16:26

edgingtonn1

Could someone remind me why 'membrane protein' seems to be missing in the PhagesDB.org Pham 'notes' section, and isn't seen as a predicted function when looking at a Phage gene list? The function is in the published Genbank files however. An example below is with Asa16. Best, -Nick Pham 36850 - No 'notes' with 'membrane protein' function? Asa16_CDS_23 Membrane Protein. From the Genbank file: gene 19751..20182 /gene="23" /locus_tag="SEA_ASA16_23" CDS 19751..20182 /gene="23" /locus_tag="SEA_ASA16_23" /codon_start=1 /transl_table=11 /product="membrane protein" /protein_id="UAJ15384.1" /translation="MDLLPVILGTVGVIVGAVLSYFGVRFTARQNAKAAKDAAAVSNR QVDVDEWRAIVGALREEVGRLTTRVENLEKKRDDDRDYIETLEAEARAHEARYRLLLR YVRDVLTWAAKIAPDHDPPNAPDPLRDDLPNERNPAHADHS"

Link to this post | posted 11 Mar, 2022 19:02

edgingtonn1

Hi Christian, Using a slight modification of your MySQL query statement, I pulled the data for all HostGenus = Arthrobacter and Microbacteria, and then tried the phamclust -t 0 -m gcs "-t 0" flag (to set the similarity threshold for a genome to join a cluster to zero). I thought it would produce a single file with an all-by-all matrix, but instead it actually produced even more cluster matrix files than when I used the default "-t 35". For both, I used the same input file. Did I do something wrong? or am I misinterpreting "-t=0"? P.S. Setting it to 100% is interesting. There are seven phamclust 'clusters' (in these phages from these two hosts, wherein all of the members have 100% GSC with each other! Best, -Nick Cohort IV Southern Connecticut State University 501 Crescent St. Department of Biology, SCI 311E New Haven, CT 06515

Link to this post | posted 11 Mar, 2022 14:51
edgingtonn1	Here is a powerful program, but there is a learning curve! http://circos.ca Here someone has tried to make it easier with a Circos web interface This one looks nice, but costs money. Best, -Nick Cohort IV Southern Connecticut State University 501 Crescent St. Department of Biology, SCI 311E New Haven, CT 06515

Link to this post | posted 20 Jan, 2022 01:11

edgingtonn1

I'm forwarding this from the JAX-GE Team: "Hello, We are writing on behalf of the education team at The Jackson Laboratory (www.jax.org/education-and-learning), where we are embarking on a project to develop new curricular resources in the areas of genetics and genomics for undergraduates. We are seeking your feedback via a brief survey to learn more about your students and curriculum and to determine if the potential exists for us to create discrete genetics and genomics content modules in support of undergraduates and their teaching faculty. About the Jackson Laboratory Founded in 1929, The Jackson Laboratory (“JAX”) pioneered the use of  mice as models for  human disease and has since earned a reputation for excellence with respect to providing mouse models and services to researchers worldwide.  As a nonprofit biomedical research institution, JAX also has 65 faculty with independent research programs that integrate deep experience in mammalian genetics with ground-breaking advances in human genomics and bioinformatics to decipher the biological and genomic causes of human disease and drive medical progress. Why are we reaching out? The Jackson Laboratory’s Genomic Education team (JAX GE) provides access to engaging educational opportunities for diverse learners spanning the continuum from high school students to research scientists and clinical professionals. We are actively exploring the potential for creating free course content and corresponding faculty support materials that can be adopted and used by undergraduate students and faculty within existing courses and curricula, with the hope of significantly broadening our reach and impact with respect to the undergraduate learner population. Our primary goal for this survey is to learn more about any of your emerging, underserved or unmet undergraduate course content needs that intersect with JAX’s science and content expertise in the realm of genetics, genomics, and bioinformatics. This anonymous survey should take approximately 10-15 minutes to complete and all respondents who wish to participate will have the opportunity to enter a drawing for a $100 Amazon gift card. Follow this link to the Survey: Take the Survey Or copy and paste the URL below into your internet browser: https://thejacksonlaboratory.qualtrics.com/jfe/preview/SV_e5M8mN1VSRjrwN0?Q_CHL=preview You will have the option to stop and restart your survey if you cannot complete it all at once. Sincerely, The JAX Genomic Education Team "

Link to this post | posted 05 Jan, 2022 19:34

edgingtonn1

I'm a new Apple M1 user now myself, and it appears that the only choice is to use the latest version of "Parallels" with a VM 'Windows Insider' version of Windows 10 ARM64. VirtualBox will not work, and it seems that it is never going to be updated to work on an ARM64 architecture! You can create a Ubuntu VM with the Ubuntu 20 LTS ARM64 OS if you are also interested in getting Ubuntu up and running. (I assume that the Ubuntu SEA-PHAGES VM circa 2017 will not work.) Wine would be another option to try now that (since version 6.0.1) it adds support for the M1 architecture, but I haven't tried it, since it was always pretty buggy for me when I tried using it with DNAMaster with the previous Apple OS's. My IT dept. is still working on the Parallels/WIN10-ARM VM set up for me so I haven't tested this setup myself yet! Best, -Nick Cohort 4 Dept. Biology Southern Connecticut State University New Haven, CT

Link to this post | posted 21 Nov, 2019 16:20
edgingtonn1	Awesome Chris–Thanks!