Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detect orthologs between genomes.

References:

• Wall, D.P., Fraser, H.B. and Hirsh, A.E. Detecting putative orthologs Bioinformatics (2013), 19:1710-1711.

• RSD Main Site: https://github.com/todddeluca/reciprocal_smallest_distance

• Module Name: RSD (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • RSD_EXAMPLES
• Example files in $RSD_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load RSD
[user@cn3144 ~]$ cp -R $RSD_EXAMPLES .
[user@cn3144 ~]$ rsd_search -q examples/genomes/Mycoplasma_genitalium.aa/Mycoplasma_genitalium.aa \
--subject-genome=examples/genomes/Mycobacterium_leprae.aa/Mycobacterium_leprae.aa \
-o Mycoplasma_genitalium.aa_Mycobacterium_leprae.aa_0.8_1e-5.orthologs.txt

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. RSD.sh). For example:

#!/bin/bash
module load RSD
cp -R $RSD_EXAMPLES .
rsd_search -q examples/genomes/Mycoplasma_genitalium.aa/Mycoplasma_genitalium.aa \
--subject-genome=examples/genomes/Mycobacterium_leprae.aa/Mycobacterium_leprae.aa \
-o Mycoplasma_genitalium.aa_Mycobacterium_leprae.aa_0.8_1e-5.orthologs.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] RSD.sh

Create a swarmfile (e.g. RSD.swarm). For example:

rsd_search -q path_to_org1.aa --subject-genome=path_to_org2.aa -o org1_org2_0.8_1e-5.orthologs.txt
rsd_search -q path_to_org1.aa --subject-genome=path_to_org3.aa -o org1_org3_0.8_1e-5.orthologs.txt
rsd_search -q path_to_org1.aa --subject-genome=path_to_org4.aa -o org1_org4_0.8_1e-5.orthologs.txt
rsd_search -q path_to_org1.aa --subject-genome=path_to_org5.aa -o org1_org5_0.8_1e-5.orthologs.txt

Submit this job using the swarm command.

swarm -f RSD.swarm [-g #] [-t #] --module RSD