The DupGen_finder was developed to identify different modes of duplicated gene pairs. MCScanX algorithm was incorporated in this pipeline.
| Authors | Xin Qiao (Xin Qiao) |
| Qionghou Li (Qionghou Li) | |
| Yupeng Wang (Yupeng Wang) | |
| Shaoling Zhang (Shaoling Zhang) | |
| Andrew H. Paterson (PGML) | |
| qiaoxinqx2011@126.com |
Figure 1: The flowchart of DupGen_finder pipeline
cd ~/software # or any directory of your choice
git clone https://github.com/qiao-xin/DupGen_finder.git
cd DupGen_finder
make
chmod 775 DupGen_finder.pl
chmod 775 DupGen_finder-unique.pl
chmod 775 set_PATH.sh
source set_PATH.shTest you can run DupGen_finder:
DupGen_finder.plDupGen_finder should print its 'help' text.
**Note**
DupGen_finder software package includes a custom MCScanX algorithm which can output sorted gff files such as Ath.gff.sorted, and is slightly different from the original MCScanX algorithm implemented in MCScanX software package.
Pre-computed BLAST results (-outfmt 6) and gene location information (GFF format) are required for running DupGen_finder successfully.
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For the target genome in which gene duplicaiton modes will be classified, please prepare two input files:
target_species.gff, a gene position file for the target species, following a tab-delimited format. For example, "Ath.gff".target_species.blast, a blastp output file (-outfmt 6) for the target species (self-genome comparison). For example, "Ath.blast".
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For the outgroup genome, please prepare two input files:
[target_species]_[outgroup_species].gff, a gene position file for the target_species and outgroup_species, following a tab-delimited format.[target_species]_[outgroup_species].blast, a blastp output file (-outfmt 6) between the target and outgroup species (cross-genome comparison).
For example, assuming that you are going to classify gene duplication modes in Arabidopsis thaliana (Ath), using Nelumbo nucifera (Nnu) as outgroup, you need to prepare 4 input files: Ath.gff,Ath.blast, Ath_Nnu.gff, Ath_Nnu.blast
gff file
Ath.gff is in the following format (tab separated):
Species_abbrev-Chr_ID gene_ID start_position end_position
The data in Ath.gff looks like this (tab separated):
Ath-Chr1 AT1G01010.1 3631 5899
Ath-Chr1 AT1G01020.1 5928 8737
Ath-Chr1 AT1G01030.1 11649 13714
Ath-Chr1 AT1G01040.2 23416 31120
Ath-Chr1 AT1G01050.1 31170 33153
The below command can be used to creat Ath_Nnu.gff:
cat Ath.gff Nnu.gff >Ath_Nnu.gffThe data in Ath_Nnu.gff looks like this (tab separated):
Ath-Chr1 AT1G01010.1 3631 5899
Ath-Chr1 AT1G01020.1 5928 8737
...
Nnu-megascaffold_32 NNU_00001-RA 57481 63788
Nnu-megascaffold_32 NNU_00002-RA 32491 41125
...
blast file
Ath.blast is in the following format:
query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
The data in Ath.blast looks like this (tab separated):
ATCG00500.1 ATCG00500.1 100.00 488 0 0 1 488 1 488 0.0 932
ATCG00510.1 ATCG00510.1 100.00 37 0 0 1 37 1 37 2e-19 73.9
ATCG00280.1 ATCG00280.1 100.00 473 0 0 1 473 1 473 0.0 876
ATCG00890.1 ATCG01250.1 100.00 389 0 0 1 389 1 389 0.0 660
ATCG00890.1 ATCG00890.1 100.00 389 0 0 1 389 1 389 0.0 660
Here is the typical parameter setting for generating the xyz.blast file:
The example file Ath.pep contains the whole genome protein sequences (FASTA format) of Arabidopsis.
- For BLAST software
# Create a reference database
makeblastdb -in Ath.pep -dbtype prot -title Ath -parse_seqids -out Ath
# Align protein query sequences against the reference database
blastp -query query_file -db database -evalue 1e-10 -max_target_seqs 5 -outfmt 6 -out xyz.blast
# For example
blastp -query Ath.pep -db Ath -evalue 1e-10 -max_target_seqs 5 -outfmt 6 -out Ath.blast- For DIAMOND software
# Create a reference database
diamond makedb --in Ath.pep -d Ath
# Align protein query sequences against the reference database
diamond blastp -d Ath -q Ath.pep -o Ath.blast -p 20 --sensitive --max-target-seqs 5 --evalue 1e-10 --quietNOTE: All above input files should be stored under the same folder (the "-i" option). For more parameters please see below.
Run the following command to get help information about DupGen_finder:
DupGen_finder.plThis command will print a full list of options:
Usage: DupGen_finder.pl -i data_directory -t target_species -c outgroup_species -o output_directory
#####################
Optional:
-a 1 or 0(are segmental duplicates ancestral loci or not? default: 1, yes)
-d number_of_genes(maximum distance to call proximal, default: 10)
#####################
The following are optional MCScanX parameters:
-k match_score(cutoff score of collinear blocks for MCScanX, default: 50)
-g gap_penalty(gap penalty for MCScanX, default: -1)
-s match_size(number of genes required to call a collinear block for MCScanX, default: 5)
-e e_value(alignment significance for MCScanX, default: 1e-05)
-m max_gaps(maximum gaps allowed for MCScanX, default: 25)
-w overlap_window(maximum distance in terms of gene number, to collapse BLAST matches for MCScanX, default: 5)
A typical command to identify different modes of duplicated gene pairs in a given species could look like this:
DupGen_finder.pl -i data -t Ath -c Nnu -o resultsHere, DupGen_finder attempts to identify the different modes of duplicated gene pairs in A.thaliana by using N.nucifera as outgroup. All required data files should be stored under this directory data. The output files will be stored under this directory results. For more details please see below. Ath: A.thaliana, Nnu: N.nucifera.
Note: We recommend that the "data_directory" or "output_directory" should be given a full path. For example, /home/the_path_to_your_data_directory/
Moreover, to eliminate redundant duplicate genes among different modes, we provide a stricter version of DupGen_finder named DupGen_finder-unique by which each duplicate gene was assigned to a unique mode after all of the duplicated gene pairs were classified into different gene duplication types. The priority of the duplicate genes is as follows: WGD > tandem > proximal > transposed > dispersed.
DupGen_finder-unique.pl -i data -t Ath -c Nnu -o results- Ath.wgd.pairs
- Ath.tandem.pairs
- Ath.proximal.pairs
- Ath.transposed.pairs
- Ath.dispersed.pairs
These files includes duplicated gene pairs derived from five modes of gene duplication, including WGD (Ath.wgd.pairs), tandem duplication (Ath.tandem.pairs), proximal duplication (Ath.proximal.pairs), transposed duplication (Ath.transposed.pairs), dispersed duplication (Ath.dispersed.pairs). The gene pairs contained in these files looks like this (tab separated):
Duplicate 1 Location Duplicate 2 Location E-value
AT1G01010.1 Ath-Chr1:3631 AT4G01550.1 Ath-Chr4:673862 5e-52
AT1G01020.1 Ath-Chr1:5928 AT4G01510.1 Ath-Chr4:642733 5e-74
AT1G01030.1 Ath-Chr1:11649 AT1G13260.1 Ath-Chr1:4542168 3e-45
AT1G01050.1 Ath-Chr1:31170 AT3G53620.1 Ath-Chr3:19880504 6e-126
AT1G01060.1 Ath-Chr1:33666 AT5G17300.1 Ath-Chr5:5690227 3e-30
It includes genes that have no homologous genes within target species.
GeneID Location
AT2G32600.1 Ath-Chr2:13833545
AT5G11810.1 Ath-Chr5:3808720
AT4G16610.1 Ath-Chr4:9354321
AT1G66520.1 Ath-Chr1:24816128
AT1G51110.1 Ath-Chr1:18935329
The number of duplicated gene pairs derived from different modes.
Types NO. of gene pairs
WGD-pairs 4352
TD-pairs 2063
PD-pairs 788
TRD-pairs 4447
DSD-pairs 16130
- Ath.collinearity
- Ath_Nnu.collinearity