orthoVar package provides functions for generating genome-wide multiple sequence alignments (msa) and finding orthologous variants between species. There are two functions in this package. orthoMSA is used to generate msa tables formatted for use in orthoFind function as an input.

orthoMSA function takes following arguments as input:

• species1: Scientific name of the species whose sequence data will be base for alignment to build upon. Homo sapiens as default. This will also take other species in future releases.

• species: A character string or character vector specifying scientific name of the species whose protein sequences will be aligned. Valid inputs are accessible with listSpecies() command.

• humanSeqFile: Path of fasta file consisting of human protein sequences. Default is NA, which downloads file from NCBI.

• seqFiles: A character string or character vector specifying path of fasta files consisting of protein sequences of other species specified in species argument. Default is NA, which downloads files from NCBI.

• annot: Annotation source. Either ncbi or ensembl.

• customOrt: A data frame consisting of gene orthology data for given species. Default is NA, which takes data from AllianceGenome: Alliance of Genome Resources (alliancegenome.org). This can either be ensembl or custom data, which should be in the same format as the data provided below, including column names:

The output is a data frame, with first two columns represent protein id and sequence for Homo sapiens. Other columns follow the same patterns, where every two columns belong to a species.

Example usage: hum_mouse <- orthoMSA(species1 = "Homo sapiens", species = "Mus musculus", customOrt = "ensembl", annot = "ensembl")

orthoFind function can be used to find orthologous variants between species. msa table generated by orthoMSA function is used as an input. Other required files are:

• Variant data (df1, df2) as data.table or data.frame, with at least following columns:

  • Refseq_ID: NCBI reference sequence id of proteins.

  • aapos: Amino acid position of variants.

  • from: Reference amino acid.

  • to: Converted amino acid.

All arguments are listed below:

• df1: Variant data for the first organism

• df2: Variant data for the second organism

• org1: Scientific name of the first organism.

• org2: Scientific name of the second organism.

• msa: msa table which is the output of orthoMSA function

• ort: Should data be filtered according to type of variant (conserved and non-conserved). Default is TRUE. Refer to paper for detailed explanation: <https://doi.org/10.1101/2021.01.07.424951>

Output is data.table with each row representing a variant-orthologous variant combination. Below is an example output: