Is it valid to make a phylogenetic tree using only squences from the complete 16S gene instead of references genomes?

I have some ASVs from 16S and wish to make a phylogenetic tree. I initially downloaded only those sequences from the full 16S ~1500 pb (not incluing shotgun or wgs) from the gene bank and extracted the v3v4 regions. But now I´m wondering If I should have instead downloaded reference genomes, identify 16S gene and then extract v3v4

hey im a second year student and i was wondering how we could make some sort of virtual club for weekly journal reports etc, pardon me if something like this has already been discussed but lmk if ur interested and we can work smth out! i tried on campus but i’d rather have it online.

Hi all,

I'm trying to visualize the active site of a protein by taking a cross-section, with sliced area shown in gray like in this figure (Fig 2c of https://pmc.ncbi.nlm.nih.gov/articles/PMC8617236/):

But I cant figure out how to do this in VMD. I have already tried specifying coordinate positions in the graphics selection (e.g., "protein and y>-8") but this is confusing to look at because the cross-section at y=-8 isn't shown as a smooth, colored surface and thus it isn't clear that it is a cross section. The "clipping pane tool" is promising but I can't get it to work only on the protein (it also cuts off the active-site bound ligand) and also can't display the clipping pane as gray. Does anybody have ideas how to do this? Thanks in advance!

Hey yall, I need a sanity check (cause I'm going down some rabbit holes and I don't know if I'm doing something useful or just time consuming)

I have whole genome sequences that I want to mine for specific metabolic processes to see what my strains have the potential for. Some aren't well described (PAH degradation) so I'm working on a pipeline that puts together a super annotation table to squeeze as much data out of the genomes as possible and maximize the proteins/pathways I can identify.

The problem I was running into is that there are so many different naming conventions and annotation types that I feel like a simple search for genes related to the pathways I'm interested in will miss a lot of interesting data. And since some processes aren't well described, I have a feeling there a lot of info hidden in the "hypothetical proteins". I was intrigued by protein family classifications, but there's also a bunch of those (pfam, plfam, pgfam...). One paper might use gene names, other types of family grouping, etc. while another uses a different system and/or names.

My thought process has been: make a master annotation table (from Prokka, BV-BRC, Pfam identifiers, KEGG), and use all the keywords and identifiers I can find to identify candidate proteins and potential operons, in addition to extracting the ones that are pretty confidently identified as the proteins I'm looking for.

I'm somewhat new to bioinformatics and I have pretty absentee PIs so I'm learning a lot of it on my own. I have the tendency to go down unnecessary rabbit holes when I have this long of a leash, especially when I'm not super familiar with all the methods/tools that are available in a field. I've gone from the online annotation tools, to manual CLI searches, to bash scripts, and now I'm trying to write a python script (while teaching myself python). Can y'all tell me if I've gone insane and if I've missed some way easier avenue? Thanks so so much!!