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RSD

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

References:

There may be multiple versions of RSD available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail RSD

To select a module, type

module load RSD/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

module load RSD
cp -R $RSD_HOME/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
Batch job on Biowulf

Create a batch input file (e.g. RSD.sh), which uses the input file 'RSD.in'. For example:

#!/bin/bash
module load RSD
cp -R $RSD_HOME/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=1 --mem=4g RSD.sh
Swarm of Jobs on Biowulf

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 -g 4 RSD.swarm 
Interactive job on Biowulf

Once an interactive session has been allocated,

sinteractive --cpus-per-task=2 --mem=4g

instructions are the same as on Helix.

Documentation