SecStrAnnotator:Analysis - Revision history

Midlik at 09:43, 16 July 2020

2020-07-16T09:43:11Z

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

	==Procedure==		==Procedure==
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	* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format \| SecStrAPI format]],		* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format \| SecStrAPI format]],
	* formatting into TSV format for further analyses.		* formatting into TSV format for further analyses.

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

	Example usage:		Example usage:

	~~bash~~ scripts/~~secstrapi_data_preparation~~/~~SecStrAPI_master~~.sh		python3 scripts/SecStrAPI_pipeline.py scripts/SecStrAPI_pipeline_settings.json --resume

	Before running, modify the ~~SETTINGS section of~~ <code>~~SecStrAPI_master~~.sh</code> to set your family of interest, data directory~~, options, paths to your template annotation~~ (~~TEMPLATE_ANNOTATION_FILE, TEMPLATE_STRUCTURE_FILE~~)~~. Unwanted steps of the pipeline can be commented out in the MAIN PIPELINE section~~.		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===		===Data analysis===
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	===Data===		===Data===

	For the Cytochrome P450 family, structures of ~~1775~~ protein domains are available, located in ~~953~~ PDB entries (updated on ~~23 March~~ 2020). The analysis was performed on a non-redundant subset containing ~~175~~ protein domains.		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://is.~~muni~~.~~cz/www/midlik/secstrannotator~~/~~CytochromesP450-20200323-without_structures~~.~~zip~~ here] (structural files not included because of their size).		The data are available [https://doi.org/10.5281/zenodo.3939133 here] (structural files not included because of their size).

	===Occurrence of SSEs===		===Occurrence of SSEs===

Midlik: /* Example case study: Cytochromes P450 */

2020-05-19T13:37:05Z

Example case study: Cytochromes P450

← Older revision		Revision as of 13:37, 19 May 2020
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	For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries (updated on 23 March 2020). The analysis was performed on a non-redundant subset containing 175 protein domains.		For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries (updated on 23 March 2020). The analysis was performed on a non-redundant subset containing 175 protein domains.

	The data are available [https://is.muni.cz~~/auth~~/www/midlik/secstrannotator/CytochromesP450-20200323-without_structures.zip here] (structural files not included because of their size).		The data are available [https://is.muni.cz/www/midlik/secstrannotator/CytochromesP450-20200323-without_structures.zip here] (structural files not included because of their size).

	===Occurrence of SSEs===		===Occurrence of SSEs===

Midlik: /* Data */

2020-04-09T15:20:32Z

Data

← Older revision		Revision as of 15:20, 9 April 2020
Line 40:		Line 40:
	===Data===		===Data===

	For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries. The analysis was performed on a non-redundant subset containing 175 protein domains.		For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries (updated on 23 March 2020). The analysis was performed on a non-redundant subset containing 175 protein domains.

	The data are available [https://is.muni.cz/auth/www/midlik/secstrannotator/CytochromesP450-20200323-without_structures.zip here] (structural files not included because of their size).		The data are available [https://is.muni.cz/auth/www/midlik/secstrannotator/CytochromesP450-20200323-without_structures.zip here] (structural files not included because of their size).

Midlik: /* Data preparation */

2020-04-09T15:15:01Z

Data preparation

← Older revision		Revision as of 15:15, 9 April 2020
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	* annotation,		* annotation,
	* multiple sequence alignment for individual SSEs,		* multiple sequence alignment for individual SSEs,
	* formatting into SecStrAPI format,		* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format \| SecStrAPI format]],
	* formatting into TSV format for further analyses.		* formatting into TSV format for further analyses.

Midlik: /* Procedure */

2020-04-09T14:15:39Z

Procedure

← Older revision		Revision as of 14:15, 9 April 2020
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	* Launch <code>rstudio</code> from the said directory		* 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 \|~~ Data preparation]]		* 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)		* 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		* Run <code>sec_str_anatomy.R</code> line by line

Midlik: /* Sequence of SSEs */

2020-04-09T12:20:53Z

Sequence of SSEs

← Older revision		Revision as of 12:20, 9 April 2020
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	File:SecStrAnnotator-cyp-sse-logo-L-.png		File:SecStrAnnotator-cyp-sse-logo-L-.png
	</gallery>		</gallery>



	<gallery mode="packed" heights=140px caption="Beta strands">		<gallery mode="packed" heights=140px caption="Beta strands">

Midlik at 11:32, 9 April 2020

2020-04-09T11:32:05Z

← Older revision		Revision as of 11:32, 9 April 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. ~~The main scripts are~~		SecStrAnnotator Suite provides scripts (Python, R, and bash) for batch annotation of the whole family and analysis of the annotation results.

	~~- <code>scripts/secstrapi_data_preparation/SecStrAPI_master.sh</code> – this bash script used to prepare data for SecStrAPI also formats the annotations into tab-separated (TSV) files readable by R~~

	- <code>scripts/R_sec_str_anatomy_analysis/secondary_structure_anatomy.R</code> – contains commands for reading the annotation results, generating plots, and performing some statistical test to compare eukaryotic and bacterial structures (or any two sets of structures)


	==Procedure==		==Procedure==
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	For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries. The analysis was performed on a non-redundant subset containing 175 protein domains.		For the Cytochrome P450 family, structures of 1775 protein domains are available, located in 953 PDB entries. The analysis was performed on a non-redundant subset containing 175 protein domains.

			The data are available [https://is.muni.cz/auth/www/midlik/secstrannotator/CytochromesP450-20200323-without_structures.zip here] (structural files not included because of their size).

	===Occurrence of SSEs===		===Occurrence of SSEs===

Midlik at 11:22, 9 April 2020

2020-04-09T11:22:31Z

← Older revision		Revision as of 11:22, 9 April 2020
Line 1:		Line 1:
	SecStrAnnotator Suite provides scripts (Python, R, and bash) for batch annotation of the whole family and analysis of the annotation results. The main scripts are		SecStrAnnotator Suite provides scripts (Python, R, and bash) for batch annotation of the whole family and analysis of the annotation results. The main scripts are

	- <code>SecStrAPI_master.sh</code> – this bash script used to prepare data for SecStrAPI also formats the annotations into tab-separated (TSV) files readable by R		- <code>scripts/secstrapi_data_preparation/SecStrAPI_master.sh</code> – this bash script used to prepare data for SecStrAPI also formats the annotations into tab-separated (TSV) files readable by R

	- <code>secondary_structure_anatomy.R</code> – contains commands for reading the annotation results, generating plots, and performing some statistical test to compare eukaryotic and bacterial structures (or any two sets of structures)		- <code>scripts/R_sec_str_anatomy_analysis/secondary_structure_anatomy.R</code> – contains commands for reading the annotation results, generating plots, and performing some statistical test to compare eukaryotic and bacterial structures (or any two sets of structures)


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	===Data analysis===		===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.		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:		Example usage:

Midlik: /* Data analysis */

2020-04-09T11:19:02Z

Data analysis

← Older revision		Revision as of 11:19, 9 April 2020
Line 34:		Line 34:
	* Launch <code>rstudio</code> from the said directory		* 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 \| Data preparation]]		* In <code>sec_str_anatomy.R</code>, set DATADIR to the path to your annotation data created in [[#Data preparation \| Data preparation]]
	* ~~Modify the family-specific settings in~~ <code>sec_str_anatomy_settings.R</code>		* 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		* Run <code>sec_str_anatomy.R</code> line by line

Midlik: /* Procedure */

2020-04-09T11:17:08Z

Procedure

← Older revision		Revision as of 11:17, 9 April 2020
Line 25:		Line 25:

	Before running, modify the SETTINGS section of <code>SecStrAPI_master.sh</code> to set your family of interest, data directory, options, paths to your template annotation (TEMPLATE_ANNOTATION_FILE, TEMPLATE_STRUCTURE_FILE). Unwanted steps of the pipeline can be commented out in the MAIN PIPELINE section.		Before running, modify the SETTINGS section of <code>SecStrAPI_master.sh</code> to set your family of interest, data directory, options, paths to your template annotation (TEMPLATE_ANNOTATION_FILE, TEMPLATE_STRUCTURE_FILE). Unwanted steps of the pipeline can be commented out in the MAIN PIPELINE section.


	===Data analysis===		===Data analysis===
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	Example usage:		Example usage:

	* Launch rstudio from ~~this~~ directory		* Launch <code>rstudio</code> from the said directory
	* ~~Set~~ the path to your annotation data ~~(DATADIR)~~ in ~~sec_str_anatomy.R~~		* In <code>sec_str_anatomy.R</code>, set DATADIR to the path to your annotation data created in [[#Data preparation \| Data preparation]]
	* Modify the family-specific settings in sec_str_anatomy_settings.R		* Modify the family-specific settings in <code>sec_str_anatomy_settings.R</code>
	* Run sec_str_anatomy.R line by line		* Run <code>sec_str_anatomy.R</code> line by line

	==Example case study: Cytochromes P450==		==Example case study: Cytochromes P450==