One of the most popular and powerful tools in bioinformatics suitable for ortholog detection is OrthoMCL. Nevertheless, it is also one of the most difficult to install and run tools, because it requires many dependencies including BLAST and MySQL database. With InsideDNA platform, we made OrthoMCL as easy as possible to work with and describe below the entire pipeline for ortholog detection in genomes of three bacterial species of Ralstonia. In total, it takes about 10 minutes to run the entire pipeline on three bacterial genomes.
1. Input data
We are going to analyse genomes for three bacterial species of Ralstonia which we have downloaded from. All three genomes can be also downloaded as a single (total size 792Kb). Typically, source data for OrthoMCL pipeline are fasta-files with either amino acid or nucleotide sequences. Moreover, you can use either annotated data (e.g. transcriptoms from NCBI) or raw data obtained with RNA-seq or single reads/paired end Illumina full genome equencing. Most often, several genomes are analyzed at once with OrthoMCL pipeline.
2. Compile all tools into a single project
3. Running orthomc AdjustFasta
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