lep_exome_analysis
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Arkaned
- Language: R
- Default Branch: master
- Size: 9.32 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Lepidoptera Orthologue Amino Acid Comparison
Introduction
This repository is a collection of code and guides created by Arkan De Lomas for using orthofinder in bioinformatics. More information on Orthofinder can be found in its repository: https://github.com/davidemms/OrthoFinder
Process
- 30+ lepidopteran species have their exomes analysed (using orthofinder) for gene sequence similarity to then be gathered into orthologues and non-orthologues.
- The data produced by Orthofinder (default run) contains a distinction between genes in each species that are orthologous and genes that are not (nonorthologous genes do not possess counterparts in other species within the dataset).
- amino acid content of orthologous and non-orthologous genes are then counted to produce frequency comparisons for each species to then deduce trends and niches within each species based on their climate, diet, and amino acid content of genes.
Description of files in repository:
The main Orthogroup python file is Orthogroup_counter.py while for non-orthologous genes there are two python files as Orthofinder organizes the non-orthologous gene results differently from the orthologous gene results.
Orthogroup_counter.py
This file produces a list of amino acid frequency in each othrologous gene for each species.
nonortholog_seqs.py
This file collates non-orth seq data from multiple columns into one colum and gathers frequency of amino acids.
nonorthsummary.py
Reads data produced by nonorthologseqs.py ('nonorthseqandaa.csv') and assigns them to species that contain those genes.
Primary_transcripts/
This folder has citations, statistics from the Orthofinder run, and some remnant data from calculating amino acid frequency for non-orthologous genes.
Owner
- Name: Arkan De Lomas
- Login: Arkaned
- Kind: user
- Location: Aberdeen, Scotland, UK
- Company: University of Aberdeen
- Repositories: 2
- Profile: https://github.com/Arkaned
Biologist who likes using technology to solve ecology and conservation related problems.
Citation (CITATION.cff)
De Lomas, Arkan (2024) Lepidoptera Exome Analysis
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