Toxshell for Comparative Genomics
This is for server side HPC rendering and comparison for ToxDB species
Gaurav Sablok
codeprog@icloud.com

toxshell analyzer
enter the gff1 file:ToxoDB-65_TgondiiME49.gff
enter the gff2 file:ToxoDB-66_TgondiiME49.gff

Prepairing the analysis for the comparative genomics of ToxDB

The number of the protein coding genes in the first gff1 file are:
46
The number of the protein coding genes in the second gff2 file are:
41
The simplified coordinates of the protein_coding_genes are written to gff_1_simplified and gff_2_simplified
The ids of the genes which are dissimilar in both the annotation are in the file gff_compare_dissimilar_ids and their indiviual ids are present in 	gff_1_ids and gff_2_ids
The similar genes are written in the file: gff_compare_similar_ids
The shared ids from the first GFF are written to the gff_1_final_compare 
The shared ids from the second GFF are written to the gff_2_final_compare 

final_sorted_ids_start_end_difference


Final Files

The final files for the comparative analysis are:
1. Simplified GFF 1: gff_1_simplified containing the simplified version
2. Simplified GFF 2: gff_2_simplified containing the simplified version
3. Similar genes: gff_compare_similar_ids
4. Dissimilar genes: gff_compare_dissimilar_ids
5. Shared ids from the first GFF: gff_1_final_compare
6. Shared ids from the second GFF: gff_2_final_compare
7. Genes differ on the first gff: gff_1_final_differ
8. Genes differ on the second gff: gff_2_final_differ
9. Genes differ on the first gff and present on the negative strand: gff_1_final_differ_negative_strand
10. Genes differ on the first gff and present on the positive strand: gff_1_final_differ_positve_strand
11. Genes differ on the second gff and present on the negative strand: gff_2_final_differ_negative_strand
12. Genes differ on the second gff and present on the positive strand: gff_2_final_differ_positive_strand