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SecStrAnnotator:Analysis

57 bytes removed, 09:43, 16 July 2020
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SecStrAnnotator Suite provides scripts (Python, R, and bash) for batch annotation of the whole family and analysis of the annotation results.
==Procedure==
* 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:
bash python3 scripts/secstrapi_data_preparationSecStrAPI_pipeline.py scripts/SecStrAPI_masterSecStrAPI_pipeline_settings.shjson --resume
Before running, modify the SETTINGS section of settings in <code>SecStrAPI_masterSecStrAPI_pipeline_settings.shjson</code> to set your family of interest, annotation template, data directory, options, paths to your template annotation etc (TEMPLATE_ANNOTATION_FILE, TEMPLATE_STRUCTURE_FILEsee <code>README.txt</code> for more details). Unwanted steps of the pipeline can be commented out in the MAIN PIPELINE section.
===Data analysis===
===Data===
For the Cytochrome P450 family, structures of 1775 1855 protein domains are available, located in 953 1012 PDB entries (updated on 23 March 7 July 2020). The analysis was performed on a non-redundant subset containing 175 183 protein domains.
The data are available [https://isdoi.muniorg/10.cz/www/midlik/secstrannotator5281/CytochromesP450-20200323-without_structureszenodo.zip 3939133 here] (structural files not included because of their size).
===Occurrence of SSEs===
318
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