Tweet
Prograns to idIdentify core genes under negative selection
I got multiple genomes for different gram-negative bacteria. What program could I use to identify specific core genes under negative selection but with smaller regions that exhibit positive selection? Is there any limitations/problems I might encounter along the way?
-
-
Do you have annotated genomes? Or just the assemblies?
If you have annotations, your project is quite similar to one project I'm working on right now...
My strategy is:
blast all genes vs each other
use R to look for gene clusters (then, you can apply the thresholds you want to decide whether a cluster has to be reported or not...)
If you don't have annotations, I would do more or less the same, instead that I would first try to make annotations using a software like glimmer...
-
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
Comment