Summation of Ks pairs for Exploration of Whole Genome Duplications -- Whole Genome Duplication detection pipeline
WGD_detection is a script implementing several bioinformatics software and calculation to visualize gene duplication events by processing the full set of coding sequences (CDS) of an organism.
INPUT: CDS file in FASTA format;
OUTPUT: kS distribution data in csv format and histogram in user-indicated working directory (set by -d).
- CDS translation to protein sequences;
- Pairwise self-BLASTP by BLASTP;
- Extraction of pairs of comparison by identity (default: 50%) and coverage (default: 30%);
- Markov chain clustering by MCL;
- Sequence Alignment of each cluster by MUSCLE;
- For each alignment, reverse translation of protein sequences back to nucleotide sequences according to the input CDS;
- Maximum likelihood phylogenetic analysis on each nucleotide sequence alignment by yn00 from PAML;
- kS correction and gene duplication event clustering;
- Data visualization
WGD_detection is developed in Python 2.x with modules and external software, and is Python 3 compatible.
While running this pipeline, a dependency check is at first performed to make sure every dependency is correctly installed.
For information about installing the dependencies, please see below. The version numbers listed below represents the version this pipeline is developed with, and using the newest version is recommended.
- Python 2.x
- Modules can be installed using pip
pip install [module_name] - Pandas v0.16.2
- BioPython v1.64
- Seaborn v0.7.0
- BLAST for LINUX ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+ v2.2.31 -- Installation guide Ubuntu users can directly install by
sudo apt-get install ncbi-blast+ - MCL v14-137
- MUSCLE v3.8.31
- YN00 v4.8 Ubuntu users can directly install by
sudo apt-get install paml
usage: WGD_detection.py [-h] [-i NUCLEOTIDE_CDS] [-I CDS_FOLDER]
[-o OUTPUT_PREF] [-d WORKING_DIR]
[--blastp BLASTP] [--makeblastdb MAKEBLASTDB]
[--muscle MUSCLE] [--mcl MCL]
[-yn00 YN00_PATH]
[--identity IDENTITY] [--coverage COVERAGE]
[--blastp_threads BLASTP_THREADS]
[--mcl_threads MCL_THREADS]
[--mcl_inflation MCL_INFLATION]
[--cluster_aln_threads CLUSTER_ALN_THREADS]
Generate kS distrbution histogram to detect Whole Genome Duplication (WGD)
events. Taking the full coding sequences of an organism as input.
optional arguments:
-h, --help show this help message and exit
-i NUCLEOTIDE_CDS Full coding sequences of the organism of interest.
-I CDS_FOLDER A directory with CDS files of different organisms
only. NOTE: This option cannot be used with -i at the
same time. Options for threadsneed to be set to
reasonable number since a maximum of 2 files canbe
running at the same time.
-o OUTPUT_PREF Prefix for the MCL clustered files.
Default: Prefix of input file.
This option is ignored if otherwise indicated when
"-I" is used.
-d WORKING_DIR Working directory to store intermediate files of each
step. Default: ./ .
--blastp BLASTP File path to blastp executable. Default:
/usr/bin/blastp .
--makeblastdb MAKEBLASTDB
File path to makeblastdb executable. Default:
/usr/bin/makeblastdb .
--muscle MUSCLE File path to MUSCLE executable.
--mcl MCL File path to MCL executable. Default: /usr/bin/mcl .
--yn00 YN00_PATH File path to yn00 executable. Default: /usr/bin/yn00 .
--identity IDENTITY Threshold of percentage identity in BLAST result.
Default: 50 .
--coverage COVERAGE Threshold of percentage alignment coverage in BLAST
result. Default: 30 .
--blastp_threads BLASTP_THREADS
Number of threads for running BLASTp. Default: 8 .
--mcl_threads MCL_THREADS
Number of threads for running MCL. Default: 1 .
--mcl_inflation MCL_INFLATION
Tune the granularity of clustering. Usually choose
from the range of [1.2, 5.0]. 5.0 makes it finely
grained and 1.2 makes clustering coarsed. Default: 2.0
.
--cluster_aln_threads CLUSTER_ALN_THREADS
Number of threads for parallelling the alignment of
clusters. Default: 8 .