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All posts created by edgingtonn1

| posted 01 Aug, 2022 18:50
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
Posted in: AnnotationMembrane proteins
| posted 01 Aug, 2022 16:26
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"
Posted in: AnnotationMembrane proteins
| posted 11 Mar, 2022 19:02
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
Posted in: Bioinformatic Tools and AnalysesDifficulty pulling large-scale data for batch GCS analysis using Pope/Mavrich 2017 scripts
| posted 11 Mar, 2022 14:51
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
Posted in: Bioinformatic Tools and AnalysesCircular Genome Visualization
| posted 20 Jan, 2022 01:11
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 "
Posted in: General Message BoardJackson Laboratory’s Genomic Education Survey
| posted 05 Jan, 2022 19:34
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
Posted in: DNA MasterDNA Master on M1 Mac
| posted 21 Nov, 2019 16:20
Awesome Chris–Thanks!
Posted in: StarteratorRelease of Starterator version 1.2
| posted 10 Apr, 2017 14:32
Hi,

It seems that the Z-scores from PECAAN differ from the Z-scores from DNAMaster for a given gene, and for the same start sites. Any idea why? Both scores for the same gene start always seem to show the same trend, so it doesn't seem like a big issue– just a curiosity for now. Which one should be in the final annotation notes? We are going with the PECAAN ones since they are all imported into DNAMaster at once.

Best,
-Nick
SCSU, New Haven CT
Posted in: PECAANPECAAN Z-scores differ from DNAMasters
| posted 22 Feb, 2017 17:26
Thanks Chris – Yup, that was the issue! I'm not sure how it ended up locked, but it was indeed locked.

Cheers,
-Nick
Posted in: PECAANRead-only Genome for User?
| posted 22 Feb, 2017 16:29
My students are having a problem editing the Mabel genome in PECAAN, with the error stating that it is “Read-only", and thus cannot be edited/annotated. The same students can edit other SCSU genomes that have been added, but not Mabel. As an Admin, I have no problems editing Mabel. Any idea why there is a permissions error even thought they are approved Institutional Users?

Best,
-Nick
Edited 22 Feb, 2017 16:31
Posted in: PECAANRead-only Genome for User?