###################################################################### README ###################################################################### ===================================== Usage Description ===================================== The module of Orthology Protein-coding genes Pairs (OPPs) identification is used to collect orthologous relationship among 15way species guided by collinear segments. Four main steps are performed as: (1) Step1: Collect the genesets located in all n-way[2way-n] collinear_segments. (2) Step2: geneset2genemap: For two species (with cucumber as ref), select the genes which located in the same collinear segment. (3) Step3: genemap_blast_filter: For each pair of genes located in the same segment, if they share no similarity (blast E-value), they will be filtered out. (4) Step4: For each pair of OPPs, we calculate its collinear segments support score (OPSS: Ortholog_Protein-coding genes_Support_Score). ===================================== Directory Contents ===================================== This directory includes README, input directory, output directory and scripts directory. The sections below include: scripts directory run.sh pl_scripts Step2.pl Step3.1.pl Step3.2.pl Step4.pl Input directory blast_results directory ref_spec.blast BBH.results pro_gff_dir directory species_pro.gff3 segments_gff3 directory n-way directory {n}way_segments.gff3 2way-n directory 2way-{n}_segments.gff3 Output directory geneset directory n-way directory spec_{n}way_geneset.table 2way-n directory spec_2way-{n}_geneset.table genemap directory n-way directory ref_spec_{n}way_good.genemap 2way-n directory ref_spec_2way-{n}_good.genemap OPPs directory Final.opps file OPPs_MAAs-based.pair file OPPs_proteins-based.pair file 2way-n_all.opps file n-way_all.opps file spec_opps directory ref_spec_n-way(2way-n).opps README file ===================================== run.sh file ===================================== ################################################################################################################################################################################## # Prepare dataset: n-way(2way-n)_segments_gff3/* produced by collinear_detection.sh # Description: # Step 1 Collect the genesets located in all n-way[2way-n] collinear_segments. # Step 2 geneset2genemap: For two species (with cucumber as ref), select the genes which located in the same colliner segment. # Step 3 genemap_blast_filter: For each pair of genes located in the same segment, if they share no similarity (blast E-value), they will be filtered out. # Step 4 For each pair of OPPs, to calculate its collinear segments support score (OPSS: Ortholog_Protein-coding genes_Support_Score) # # Dependency tools: bedtools2-master, pl_scripts/*.pl, BBH.pair(obtained by blastp all_vs_all and extract BBH (Bidirectional Best Hits) relationships ) # Usage: sh collinear.sh # Input: n-way[2way-n]_collinear.gff3, spec_pro_gff3 including protein-coding genes annotation # Output: Final.opps # output with six columns as ref_geneID, spec_geneID, M_score (MAAs-based), P_score (proteins-based), BBH_score?(0:no, 2:yes) and OPSS_score (= M_score + P_score + BBH_score)' ################################################################################################################################################################################### ===================================== scripts directory ===================================== This directory provides the dependency four perl scripts required in run.sh. (1) Step2.pl was used to perform geneset2genemap required in step2 of run.sh ################################################################################################# # This script can be used to prepare genemap.table file used in OPPs_identify.sh as Step2. # n-way[2way-n].genemap.table: 3 columns including segmentID, ref_geneID, spec_geneID. # Usage: perl Step2.pl ref_geneset.table spec_geneset.table > ref_spec_genemap.table. # Input: ref_geneset.table, spec_geneset.table # Output: ref_spec_genemap.table ################################################################################################# (2) Step3.1.pl was used to prepare good.genemap file in step3.1 of run.sh ######################################################################################################### # This script can be used to prepare good.genemap file used in OPPs_identify.sh as Step3.1. # good.genemap: 3 columns including segmentID, ref_geneID, spec_geneID # Usage: perl Step3.1.pl ref_spec.genemap ref_spec.blast blast_evalue_cutoff > ref_spec_good.genemap # Input: (1) ref_spec.genemap; (2) ref_spec.blast; (3) blast_evalue_cutoff # Output: ref_spec_good.genemap with three columns as as segmentID, ref_geneID and spec_geneID ######################################################################################################### (3) Step3.2.pl was used to prepare good.genemap file in step3.2 of run.sh ######################################################################################################################### # This script can be used to collect the nway[2way-n] information for each OPPs used in OPPs_identify.sh as Step3.2 # Usage: perl Step3.2.pl ref_spec_n-way[2way-n]_good.genemap spec n-way[2way-n] > n-way[2way-n]_all.opps # Input: [1] ref_spec_n-way[2way-n]_good.genemap;[2] spec; [3] n-way[2way-n] # Output: n-way[2way-n]_all.opps # output with 5 Columns as: (1)ref_geneID;(2)spec_geneID;(3)spec;(4)n-way(2way-n);(5)segmentID ######################################################################################################################### (4) Step4.pl was used to prepare good.genemap file in step3.2 of run.sh ##################################################################################################################################################################################### # This script can be used to calculate OPSS (Orthology_Protein-coding genes_Support_Score) for each OPPs used in OPPs_identify.sh as Step4 # Usage: perl Step4.pl OPPs_MAAs-based.pair OPPs_proteins-based.pair BBHs.pair > Final.opps # Input: # (1) OPPs_MAAs-based.pair: the OPPs results obtained by using MAAs as genomic markers as above steps # (2) OPPs_proteins-based.pair: the OPPs results obtained by using protein-coding genes as genomic markers to perform above all steps # (3) BBHs.pair: BBH.results were obtained by blastp all_vs_all and extract BBH (Bidirectional Best Hits) relationships with BBH_extract.pl # (4) p_weight: indicating a [0,1] number as weight of score obtained by protein-based method # Output: Final.opps # Final.opps: six columns as as ref_geneID, spec_geneID, M_score (MAAs-based), P_score (proteins-based), BBH_score?(0:no, 2:yes) and OPSS_score (= M_score + P_score + BBH_score) ##################################################################################################################################################################################### ===================================== Input directory ===================================== This directory provides: (1) blast_results obtained by blast_all_vs_all. (2) segments_gff3 produced by collinear_detection.sh. (3) pro_gff3 (indicating the protein-coding genes annotation information) extracted from genome annotation files. ===================================== Output directory ===================================== This directory provides: (1) geneset files as n-way[2way-n]_geneset.table with two columns as geneID and multipliconID (segmentID). (2) genemap files as ref_spec_n-way[2way-n]_good.genemap with 5 Columns as: (1)ref_geneID;(2)spec_geneID;(3)spec;(4)n-way(2way-n);(5)segmentID. (3) OPPs directory provides: [3.1] Final.opps with 6 columns as as ref_geneID, spec_geneID, M_score, P_score, BBH_score and OPSS_score. [3.2] n-way(2way-n)_all.opps is OPPs results guided by two levels of collinear segments, with 4 Columns as ref_geneID, spec_geneID, spec, way and segmentID. [3.3] OPPs_MAAs-based.pair is the total OPPs results, with with 4 Columns as ref_geneID, spec_geneID, spec, way and segmentID. [3.4] OPP_proteins-based.pair is the OPPs results obtained by using protein-coding genes as genomic markers instead of MAAs and performing the same pipeline. [3.4] spec_opps is the OPPs for Cucumber and one of other 14 species in different collinear levels (n-way and 2way-n), with 4 Columns as ref_geneID, spec_geneID, spec, way and segmentID. two types of collinear segments files as table and gff3 files, and the segments at two different levels (n-way and 2way-n) are displayed individually. ===================================== README file ===================================== It is this file.