3.53.3

ORGANISMS ▼ SEARCHES ▼ TOOLS & SERVICES ▼ WORKSPACES ▼ HELP ▼ ABOUT ▼

Find a gene, genome, microarray, etc

▼

The BV-BRC cluster will be undergoing maintenance on August 13 from 7:00 a.m. – 3:00 p.m. (Chicago Time). Site access, Workspace, and job submission should not be affected but job execution may be delayed. The BV-BRC Copilot service will be unavailable during the maintenance. -- BV-BRC Team

Uploads 0 0 0%

Jobs

Protein Family Sorter

For further explanation, please see the Service Quick Reference Guide and Tutorial.

Select Genome

Genome

Select Genome Group

Genome Group

Disabled: please login to enable genome group selection

Select Family Type

Family Type

Selected genomes

Place genome(s) here using the arrow buttons.

●Search

Overview¶

The bacterial Protein Family Sorter Service tool enables researchers to examine the distribution of protein families across a set of user-selected genomes. Results are displayed in a page showing all the families associated with the selected genomes, plus filter controls and an interactive heatmap.

Select Family Type¶

Family Type¶

Dropdown list of options of protein family types to use in the comparison:

Cenus-specific families(PLfams): The genus-specific protein families are computed using only proteins within a genus and more stringent criteria (MCL inflation = 3.0). This provides higher sequence similarity and better specificity while performing within-genus/species or close strain comparisons.

Cross-genus families(PGfams): The cross-genera protein families are computed by clustering representative proteins from the genus-specific families with slightly relaxed criteria (MCL inflation = 1.1). This allows cross-genera or distant homologs to cluster together, which is necessary to support cross-genera comparative analysis across all microbial genomes.

FIGFams: FIGfams are sets of isofunctional homologs, i.e. set of rotein sequences that are similar along their full length and believed to implement the same function. FIGfams are derived from a collection of functional subsystems, as well as correspondences between genes in closely related strains.