Editing SecStrAnnotator:Analysis

SecStrAnnotator Suite provides scripts (Python, R) for batch annotation of the whole family and analysis of the annotation results.

==Procedure==

===Data preparation===

The directory <code>scripts/secstrapi_data_preparation/</code> contains a pipeline for annotating the whole protein family, including: 

* downloading the list of family members defined by CATH and Pfam, 
* downloading their structures, 
* selecting a non-redundant set, 
* annotation, 
* multiple sequence alignment for individual SSEs, 
* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format | SecStrAPI format]], 
* formatting into TSV format for further analyses.

The whole pipeline can be executed by <code>scripts/SecStrAPI_pipeline.py</code>

Example usage:

  python3 scripts/SecStrAPI_pipeline.py scripts/SecStrAPI_pipeline_settings.json --resume

Before running, modify the settings in <code>SecStrAPI_pipeline_settings.json</code> to set your family of interest, annotation template, data directory etc (see <code>README.txt</code> for more details).

===Data analysis===

The directory <code>scripts/R_sec_str_anatomy_analysis/</code> contains a pipeline for statistical analysis of the annotation results on the whole protein family, including:

* reading the annotation results from TSV,
* generating plots,
* performing statistical test to compare eukaryotic and bacterial structures (or any two sets of structures).

Example usage:

* Launch <code>rstudio</code> from the said directory
* In <code>sec_str_anatomy.R</code>, set DATADIR to the path to your annotation data created in [[#Data preparation]]
* In <code>sec_str_anatomy_settings.R</code>, modify the family-specific settings (list of helices and strands)
* Run <code>sec_str_anatomy.R</code> line by line

==Example case study: Cytochromes P450==

===Data===

For the Cytochrome P450 family, structures of 1855 protein domains are available, located in 1012 PDB entries (updated on 7 July 2020). The analysis was performed on a non-redundant subset containing 183 protein domains.

The data are available [https://doi.org/10.5281/zenodo.3939133 here] (structural files not included because of their size).

===Occurrence of SSEs=== 

The ''occurrence'' describes in what percentage of the structures a particular SSE is present.

<div><ul> 
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence.png | thumb | 500px | Occurrence of particular SSEs in the whole set.]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence-Bact-Euka.png | thumb | 500px | Occurrence of particular SSEs – comparison of bacterial and eukaryotic structures.]] </li>
</ul></div>

===Length of SSEs===

The ''length'' of an SSE is measured as the number of residues. The following violin plots show the distribution of length for each SSE.

<div><ul> 
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length.png | thumb | 500px | Length distribution of particular SSEs in the whole set. ]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length-Bact-Euka.png | thumb | 500px | Length distribution of particular SSEs – comparison of bacterial and eukaryotic structures. ]] </li>
</ul></div>

===Sequence of SSEs===

The amino acid sequences for each SSE can be aligned and used to produce a sequence logo. Where the sequence conservation is sufficient, we can establish a generic numbering scheme: the most conserved residue in helix X serves as its reference residue and is numbered as @X.50. The remaining residues in the helix are numbered accordingly.

<gallery mode="packed" heights=140px caption="Helices">
File:SecStrAnnotator-cyp-sse-logo-A-.png
File:SecStrAnnotator-cyp-sse-logo-A.png
File:SecStrAnnotator-cyp-sse-logo-B.png
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File:SecStrAnnotator-cyp-sse-logo-B--.png
File:SecStrAnnotator-cyp-sse-logo-C.png
File:SecStrAnnotator-cyp-sse-logo-D.png
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File:SecStrAnnotator-cyp-sse-logo-G.png
File:SecStrAnnotator-cyp-sse-logo-H.png
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File:SecStrAnnotator-cyp-sse-logo-K--.png
File:SecStrAnnotator-cyp-sse-logo-L.png
File:SecStrAnnotator-cyp-sse-logo-L-.png
</gallery>



<gallery mode="packed" heights=140px caption="Beta strands">
File:SecStrAnnotator-cyp-sse-logo-1-0.png
File:SecStrAnnotator-cyp-sse-logo-1-1.png
File:SecStrAnnotator-cyp-sse-logo-1-2.png
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File:SecStrAnnotator-cyp-sse-logo-1-5.png
File:SecStrAnnotator-cyp-sse-logo-2-1.png
File:SecStrAnnotator-cyp-sse-logo-2-2.png
File:SecStrAnnotator-cyp-sse-logo-3-1.png
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File:SecStrAnnotator-cyp-sse-logo-5-1.png
File:SecStrAnnotator-cyp-sse-logo-5-2.png
File:SecStrAnnotator-cyp-sse-logo-6-1.png
File:SecStrAnnotator-cyp-sse-logo-6-2.png
</gallery>

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