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https://github.com/applicativesystem/domain-graphs
extracting and analyzing interpro domains for domain based graphs
https://github.com/applicativesystem/domain-graphs
bioinformatics genome-analysis genome-annotation-analysis genome-domains genome-informatics interpro interpro-domains
Last synced: 19 days ago
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extracting and analyzing interpro domains for domain based graphs
- Host: GitHub
- URL: https://github.com/applicativesystem/domain-graphs
- Owner: applicativesystem
- License: mit
- Created: 2024-08-17T18:38:09.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-08-17T18:40:28.000Z (5 months ago)
- Last Synced: 2024-11-10T20:18:05.832Z (about 2 months ago)
- Topics: bioinformatics, genome-analysis, genome-annotation-analysis, genome-domains, genome-informatics, interpro, interpro-domains
- Language: Python
- Homepage:
- Size: 2.93 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
#### domain-graphs
- This repository contains a function which will prepare the domain graphs analysis, if you will specify a domain or an interpro, it will give you all the parent and the child for the directed and undirected graphs modelling.
- I implemented a string pattern search algorithm to make the search faster.
```
# for searching all the child categories of the IPR domains
IPRNetworkPlot("/Users/gauravsablok/Desktop/ipr_analyzer.txt", \
arg_IPR = "IPR000008", arg_type = "interpro")
[['IPR014705',
'IPR028692',
'IPR030537',
'IPR033884',
'IPR037300',
'IPR037301',
'IPR037302',
'IPR037303',
'IPR047897']]
# for searching all the child domains of the specific category
IPRNetworkPlot("/Users/gauravsablok/Desktop/ipr_analyzer.txt", \
arg_domain = "C2 domain", arg_type = "domain")
[['Synaptotagmin-17, C2B domain',
'Synaptotagmin-13, C2B domain',
'Synaptotagmin-12, C2B domain',
'Calpain C2 domain',
'Perforin-1, C2 domain',
'Toll-interacting protein, C2 domain',
'Protein Unc-13, C2B domain',
'Synaptotagmin-like protein 4/5, C2A domain',
'Synaptotagmins 15/17, C2A domain']]
```
Gaurav Sablok