ORthology Inference using Synteny (ORIS) Pipeline

References

• Conant GC. 2009. Neutral evolution on mammalian protein surfaces. Trends Genet. 25:377–381.
  
• Bekaert M, Conant GC. 2011. Transcriptional robustness and protein interactions are associated in yeast. BMC Syst. Biol. 5:62.
• Bekaert M, Conant GC. 2014. Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks. PLoS One. 9:e87115.

Example workflow for orthology inference between two genomes 1 and 2

Step 1: Homology search

• Download GenomeHistory 2.0
• Extract lists of gene names from fasta files. Use command such as:
  grep ">" genome1.DNA.fa |egrep -o '^>(\w|\d|\.){1,20}' |egrep -o '(\w|\d|\.){1,20}' >genome1_genelist.txt
  
• Run GenomeHistory three times: genome 1 against itself, genome 2 against itself, and genome 1 versus genome 2.

Step 2: Prepare input files

• Run make_orthology_inf_files.pl
• Will need gff files for each genome.

Step 3: Orthology inference

• Download map_orthology
  cd map_orthology
make