gene_loss's Introduction
#here are brief descriptions of the code and data associated with Woodruff 2019 "Patterns of putative gene loss suggest rampant developmental system drift in nematodes" #if there are any questions about this please contact me at [email protected] #these are versions of all retreived sequences and annotations retrieved_genomes_versions.txt #this renames protein set files and adds species-specific prefixes to gene ids prepare_protein_sets.sh #these scripts discard alternative splice variants aside from the longest isoform per gene canonical_filter_elegans.py canonical_filter_remanei-latens.py canonical_filter_t.py #these are the blastp commands generated by OrthoFinder used for orthology assignment all_by_all_blastp_commands.txt #this is the OrthoFinder command used for orthology assignment orthofinder_command.txt #this script retrieves orthogroups found in all species but one get_species-specific_gene_losses.sh #this script retrieved best reciprocal blast hits reciprocal_blast_hits.py #this script replaces OrthoFinder gene id's with assembly gene id's replace_seq_ids.sh #these are the best reciprocal blastp hits best_reciprocal_blast_hits.zip #this script extracts sequences from a multifasta file (not my original script) fasta_filter.pl #this was used to find tblastn hits outside of predicted coding regions filter_tblastn_hits.sh #these are the tblastn commands tblastn_commands.txt #these are the C. elegans constituents of lost orthogroups that were used to connect lost genes with WormBase and transcriptomic data elegans_constituents_of_lost_orthogroups.zip #this is the retreived WormBase Anatomy, Life Stage, Phenotype, Interaction, and Reference Count data wormbase_simplemine.txt #this command was used to find all Pfam domains in all C. elegans proteins hmmer_command.txt #these are the Pfam domains associated with C. elegans proteins elegans_domains.txt #this counts the number of Pfam domains per C. elegans protein domain_counts.R #this was used to connect wormbase and boeck et al. 2016 transcriptomic data with putative lost genes connect_lost_genes_wormbase_boeck_transcript.sh #this is the final WormBase and transcriptomic data set lost_genes_wormbase_boeck.tsv #this was used to analyse the WormBase and transcriptome data wormbase_boeck_analysis.R #this was used to define essential, inessential, and genes without phenotypes among the lost genes essential_genes.sh #this is the list of essential phenotypes essential_phenotypes.txt #the number of species-specific lost orthologous groups across Caenorhabditis all_caeno_og.tsv #the number of species-specific lost orthologous groups across the Elegans group elegans_group_og.tsv #this makes figure 2 figure_2.R #number of essential genes among the C. elegans constuents of lost orthologous groups across Caenorhabditis elegans_constituents_of_lost_og_phen_data_all_caeno.tsv #number of essential genes among the C. elegans constuents of lost orthologous groups across the Elegans group elegans_constituents_of_lost_og_phen_data_elegans_group.tsv #this makes figure 3 figure_3.R #this makes the supplemental figures supplemental_figures.R #this makes the data for supplemental figure 6 supplemental_figure_6.sh #genome assembly metrics for the genomes used in this study genome_statistics.tsv
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