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Bioinformatics - FSA
Instructions on how to run (and, if needed, install a customized version of) FSA
FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
1. Running FSA on Thunder
Location: /mmfs1/thunder/projects/ccastest/training/examples/FSA_example
Example: Conduct a multiple alignment on a set of sequences
File list:
· fsa_job.pbs: job submission script
· tRNA.aln1.fasta: a set of tRNA sequences in fasta format
Steps:
· Copy the example directory to your SCRATCH directory
o “cp -r /mmfs1/thunder/projects/ccastest/training/examples/FSA_example $SCRATCH”
· Go to the copied directory
o “cd $SCRATCH/FSA_example”
· Edit the job submission script as needed, then submit the job
o “qsub fsa_job.pbs”
2. Install Customized FSA on Thunder
Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.
Summary
(a) "Fixed-size Chunking" strategy for parallelization. No options in commands.
(b) "--with-mummer" or "--with-exonerate" options to ./configure before compilation enables aligning long sequences. But need install mummer or exonerate.
Details
In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME” is your username on Thunder.
(a) Install
· Go to the SOFTWARE directory:
o "cd /mmfs1/home/USERNAME/SOFTWARE"
· Download FSA, unzip and go to the unzipped directory: (refer to http://fsa.sourceforge.net)
o "wget https://sourceforge.net/projects/fsa/files/fsa-1.15.9.tar.gz"
o "tar -xzvf fsa-1.15.9.tar.gz"
o "cd fsa-1.15.9"
· Configure and specify the install location:
o "./configure --prefix=/gpfs1/home/USERNAME/SOFTWARE/fsa_install_here --with-mummer"
· Build and install:
o "make && make install"
(b) Test
· Make a test directory and go into it:
o "cd /mmfs1/thunder/scratch/USERNAME"
o "mkdir FSA_example"
o "cd FSA_example"
· Copy one example test data from source directory to current location:
o "cp /mmfs1/home/USERNAME/SOFTWARE/fsa-1.15.9/examples/tRNA.aln1.fasta ."
· Write and submit the job
o "qsub fsa_job.pbs"
------------------------------------------- file fsa_job.pbs -------------------------------------------
#!/bin/bash
#PBS -q default
#PBS -N FSA_Test
#PBS -l select=1:mem=10gb:ncpus=4
#PBS -l walltime=02:00:00
## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”
#PBS -W group_list=x-ccast-prj
cd $PBS_O_WORKDIR
##set path to binaries
export MY_FSA=/mmfs1/home/USERNAME/SOFTWARE/fsa_install_here/bin
$MY_FSA/fsa tRNA.aln1.fasta >tRNA.aln1.mfa
exit 0