SecStrAnnotator:Analysis: Difference between revisions
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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 | |||
- <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>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) | |||
==Example case study: Cytochromes P450== | |||
===Data=== | |||
The family contains 1775 protein domains located in 953 PDB entries. The analysis was performed on a non-redundant subset containing 175 protein domains. | |||
===Occurrence of SSEs=== | |||
The ''occurrence'' describes in what percentage of the structures a particular SSE is present. | |||
TODO: figure occurrence + occurrence-Bact-Euka | |||
===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. | |||
TODO: figure length + length-Bact-Euka (+box plots?) | |||
===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. | |||
TODO: logos | |||
Revision as of 11:39, 20 March 2020
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
- SecStrAPI_master.sh - this bash script used to prepare data for SecStrAPI also formats the annotations into tab-separated (TSV) files readable by R
- secondary_structure_anatomy.R - 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)
Example case study: Cytochromes P450
Data
The family contains 1775 protein domains located in 953 PDB entries. The analysis was performed on a non-redundant subset containing 175 protein domains.
Occurrence of SSEs
The occurrence describes in what percentage of the structures a particular SSE is present.
TODO: figure occurrence + occurrence-Bact-Euka
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.
TODO: figure length + length-Bact-Euka (+box plots?)
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.
TODO: logos