Secondary Structure

An additional method to understand the functional effects of transcripts is to analyze protein secondary structure.

Brewery was used to predict secondary structure in 3 classes: alpha helix, beta sheets, and the rest.

NOTE: Secondary structure analysis can take a long time. Unless absolutely necessary, we recommend to turn this feature off during analysis.

Usage

Input - /Genes/GENE/Transcripts/x_protein.fa

Output - /Genes/GENE/Transcripts/x_protein.fa.ss3

Output Folder Structure

| -- Genes/
    | -- GENE/
        | -- Transcripts/
            | -- x_protein.fa.ss3
            ...