Homo Sapien Genome Analysis

General
1

(base) Sun Mar 10 11:20:47 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ pwd
/home/illy/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13
(base) Sun Mar 10 11:20:50 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ tabname
Enter the name for the terminal tab: GRCh38.p13
(base) Sun Mar 10 11:21:02 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ ls
Annotation_comparison
annotation_hashes.txt
assembly_status.txt
GCF_000001405.39_GRCh38.p13_assembly_regions.txt
GCF_000001405.39_GRCh38.p13_assembly_report.txt
GCF_000001405.39_GRCh38.p13_assembly_stats.txt
GCF_000001405.39_GRCh38.p13_assembly_structure
GCF_000001405.39_GRCh38.p13_cds_from_genomic.fna.gz
GCF_000001405.39_GRCh38.p13_feature_count.txt.gz
GCF_000001405.39_GRCh38.p13_feature_table.txt.gz
GCF_000001405.39_GRCh38.p13_genomic.fna.gz
GCF_000001405.39_GRCh38.p13_genomic_gaps.txt.gz
GCF_000001405.39_GRCh38.p13_genomic.gbff.gz
GCF_000001405.39_GRCh38.p13_genomic.gff.gz
GCF_000001405.39_GRCh38.p13_genomic.gtf.gz
GCF_000001405.39_GRCh38.p13_protein.faa.gz
GCF_000001405.39_GRCh38.p13_protein.gpff.gz
GCF_000001405.39_GRCh38.p13_pseudo_without_product.fna.gz
GCF_000001405.39_GRCh38.p13_rm.out.gz
GCF_000001405.39_GRCh38.p13_rm.run
GCF_000001405.39_GRCh38.p13_rna.fna.gz
GCF_000001405.39_GRCh38.p13_rna_from_genomic.fna.gz
GCF_000001405.39_GRCh38.p13_rna.gbff.gz
GCF_000001405.39_GRCh38.p13_translated_cds.faa.gz
Homo_sapiens_AR109.20211119_annotation_report.xml
index.html
md5checksums.txt
README_Homo_sapiens_annotation_release_109.20211119
README_patch_release.txt
README.txt
RefSeq_transcripts_alignments
(base) Sun Mar 10 11:21:06 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ vi geneanalysis.py
(base) Sun Mar 10 11:21:45 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_0000014

(base) Sun Mar 10 11:25:18 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ vi geneanalysis.py
(base) Sun Mar 10 11:28:13 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ vi geneanalysis.py
(base) Sun Mar 10 11:28:24 illy@Fortitude ~/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13 :gear: $ python3 geneanalysis.py
Opening /home/illy/homo_sapien/ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gtf.gz…
Processing file in chunks…
Summary: {‘gene’: 61215, ‘transcript’: 177497, ‘exon’: 1998918}
{‘gene’: 61215, ‘transcript’: 177497, ‘exon’: 1998918}

MatPlot graph on distribution

Screenshot from 2024-03-10 11-51-36
Screenshot from 2024-03-10 11-51-36797×873 40.5 KB

R analysis …

I’ve distilled my strategy for leveraging the genomic data I’ve analyzed—specifically, the counts of genes, transcripts, and exons from the GRCh38.p13 human genome—into information streams, while being mindful of ethical standards.

  1. Bioinformatics Tools and Services: I plan to offer analysis services, such as gene annotation and expression analysis, to research institutions and pharmaceutical companies. I’m also creating bioinformatics software tailored to large-scale genomic data, which I’ll license out in a co-op. Trad or DAO depending.

  2. Genetic Testing and Personalized Medicine: By partnering with biomedical companies, I aim to develop genetic tests for disease predispositions and tailor treatments in personalized medicine, particularly in oncology.

  3. Educational Resources and Workshops: I’m working on online courses and workshops in genomics and bioinformatics for students, researchers, and professionals, providing practical experience with the data I’ve processed.

  4. Consultancy in Genomic Research: Leveraging my expertise, I offer consultancy services for genomic research projects and assist in grant writing and project design.

Ethical Considerations: It’s vital to me to ensure privacy and data protection, maintain transparency in how genetic data is used, and strive for access and equity in all my ventures.

In summary, by strategically applying my insights and maintaining ethical integrity, I aim to create valuable and responsible offerings in the functional genomics space.