Description

Gene-Cluster Discovery, Annotation and Visualization.

Description

Performs end-to-end analysis of gene clusters—such as photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral marker genes (e.g., capsid, polymerase, integrase)—from genomes and metagenomes. It parses Basic Local Alignment Search Tool (BLAST) results in tab-delimited format produced by tools like NCBI BLAST+ and Diamond BLASTp, filters Open Reading Frames (ORFs) by length, detects contiguous clusters of reference genes, optionally extracts genomic coordinates, merges functional annotations, and generates publication-ready arrow plots. The package works seamlessly with or without the coding sequences input and skips plotting when no functional groups are found. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

README.md

cran.r-project.org

gclink: Gene-Cluster Discovery, Annotation and Visualization

Overview

gclink performs end-to-end analysis of gene clusters (e.g., photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral genes) from (meta)genomes. It provides:

Parsing of Basic Local Alignment Search Tool (BLAST) results in tab-delimited format produced by tools like NCBI BLAST+ and Diamond BLASTp
Contiguous cluster detection
Publication-ready visualization

Key Features

Adaptive Workflow

Works with or without coding sequences input
Skips plotting when functional grouping is absent
Supports custom gene lists for universal cluster detection

Cluster Detection

Density-based identification via AllGeneNum and MinConSeq parameters
Handles incomplete gene annotation coverage
Optional insertion of hypothetical ORFs at cluster boundaries

Visualization

Publication-ready arrow plots with customizable based on gggenes:
- Color themes
- Functional group levels
- Genome subsets

Installation

# Install from CRAN
install.packages("gclink")

# Install from GitHub
if (!require("devtools")) install.packages("devtools")
devtools::install_github("LiuyangLee/gclink")

Case 1: Using blastp result

# Case 1: Using blastp result with Full pipeline (Find Cluster + Extract FASTA + Plot Cluster)
library(gclink)
data(blastp_df)
data(seq_data)
data(photosynthesis_gene_list)
data(PGC_group)
gc_list <- gclink(in_blastp_df = blastp_df,
                  in_seq_data = seq_data,
                  in_gene_list = photosynthesis_gene_list,
                  in_GC_group  = PGC_group,
                  AllGeneNum = 50,
                  MinConSeq  = 25,
                  apply_length_filter = TRUE,
                  down_IQR   = 10,
                  up_IQR     = 10,
                  orf_before_first = 0,
                  orf_after_last = 0,
                  levels_gene_group = c('bch','puh','puf','crt','acsF','assembly','regulator',
                                        'hypothetical ORF'),
                  color_theme = c('#3BAA51','#6495ED','#DD2421','#EF9320','#F8EB00',
                                  '#FF0683','#956548','grey'),
                  genome_subset = NULL)
gc_meta = gc_list[["GC_meta"]]
gc_seq = gc_list[["GC_seq"]]
gc_plot = gc_list[["GC_plot"]]
head(gc_meta)   # Cluster metadata
head(gc_seq)    # FASTA sequences
print(gc_plot)  # Visualization

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output (e.g., head(`blastp_df`))

qaccver	saccver	pident	length	mismatch	gapopen	qstart	qend	sstart	send	evalue	bitscore
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_67	enzymerhodopsin_XP_002954798.1_Volvox_carteri	26.6	576	343	15	157	666	332	893	8.18e-41	161
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_113	petB_Candidatus_Methylomirabilis_oxyfera_DAMO_1671_MOX	76.6	248	58	0	14	261	9	256	5.43e-149	417
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_114	petC_Candidatus_Nitronauta_litoralis_G3M70_16785_NLI	50.8	177	73	2	8	184	27	189	3.83e-59	184
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_523	cruC_Humisphaera_borealis_IPV69_18620_HBS	31.5	365	208	11	42	378	48	398	1.45e-41	151
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_616	rfpB_KL662192_1_938	33.0	227	137	3	4	223	3	221	2.53e-32	124
Kuafubacteriaceae--GCA_016703535.1---JADJBV010000002.1_754	bchI_p_Myxococcota--c_WYAZ01--o_WYAZ01--GCA_016703535.1---JADJBV010000002.1_754	100.0	343	0	0	1	343	1	343	4.73e-249	677

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

SeqName	Sequence
Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_1 # 3 # 266 # 1 # ID=85_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.807	CCGGACGCGCCGCCCGCCCCGAAGGCCCCGCCGGCCGCCCCCACCTATCCGCTCGAAGGCGCGCTCGGTATCAGCCGCGTGCGCCTCGTGCGCGCCACGCCCTGCGGCCTCACCGGCCGCGAGCTCGGCGCCGGCGAGGAGGCCCTCCTCGTCCACTTCGACGACGGACGCCCGCCCCTCGCGGTCGCCCCCGACGCGCTCCCGACGCCCCCCGGCGACGGGACGCCCCCCACCGGCGCTCCGCCGGAAGGAGACCCCGCATGA
Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_2 # 263 # 490 # 1 # ID=85_2;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.737	ATGACCCGCCCCGAAGACGCCCCGCCCACCCACGAAGCCGCGGACCGCGCCGTGCGCTCCCTCTTCCAGATCGGTCGCCTCTGGGCCTCCCACGGCCTCGAGATGGGTCGCATGACCTTGCGGACCGCCGCCAAGACCCTCGAGAGCACCGCCGAGACCCTCGAGGACCTCTCCCAGCGCGTCGCCCCCGACGACGAGCGCCCCGCGGACGAACGCGCCGCCGACTGA
Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_3 # 667 # 2184 # -1 # ID=85_3;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.775	ATGAGCGCGATCGAAGGGACCCGGCCTCGGGACGGCGAGGCCCGCATGCCCGTGGAGGCGACCCCCGTGGAGGCCATCGGGGGCCTCGTCGCCCGGGCGCGTGACGCCGGCTTCGACCACGCGGCCCGGCCCCTCGCCGAGCGCGCGGGGCTGCTGCGCGCGCTCGCGGACGCCATCCTCGCCGACGGGGAGGCCATCGTCGCGCTCCTCGAGGAGGAGACGGGCAAGCCGGCGGCGGAGGCGTGGCTCCACGAGGTCGTGCCGACGGCGGACCTCGGGAGCTGGTGGAGCAGCCAGGGGCCGGCGCACCTCGCGACGGAAGCCGTGCGCCTCGACCCGCTCGCCTACCCTGGCAAGCGCGCGCGCGTCGAGGTGGTCCCGCGTGGCGTCGTGGCGCTGATCACGCCTTGGAACTTCCCGGTGGCGATCCCGCTGCGGACGCTCTTCCCGGCGCTCCTCGCGGGCAACGGCGTCGTCTGGAAGCCGTCCGAGCACACGCCGCGGGTGGCGGCGCGCGTGCACGGGATCGTGCGCGAGGTCTTCGGGCCGGACCTGGTCGAGCTGGTGCAGGGCGCCGGCGCGCAGGGGGCGGCGCTGGTCGAGGCGGACGTGGACGCGGTGGTGTTCACGGGCAGCGTGGCGACCGGGCGGAAGGTCGGCGCGGCGGCGGGGCGGGCGCTCACGCCGGCGTCGCTCGAGCTCGGCGGCAAGGACGCGGCCGTGGTGCTCGACGACGCGGACCTGGAGCGCACGGCCCGGGGCCTGCTCTGGGCGGCGATGGCGAACGCGGGGCAGAACTGCGCCGGGCTCGAGCGCGTCTACGCGGTGGCGGAGGTCGCCGGCCCGCTGAAGGCGCGGCTCGGTGAGCTGGCCGGAGAGCTGGTGCCCGGGCGCGACGTGGGGCCGCTGGTGACCGAGGCGCAGCTCGCGACGGTGGAGCGGCACGTGCGCGAGGCGGTCGACGGGGGCGCGGAGGTGCTGGCCGGCGGCGAGCGGCTCGAGCGGGGCGGGCGCTGGTTCGCGCCGACCGTGCTGGCGGAGGTCGAGCCGTCTTCGGCGGCGCTCCGGGAGGAGACGTTCGGGCCGGTGGTCGTCGTGCAGACGGTGGCGGACGAGGCGGCGGCCGTGGCGGCGGCGAACGACTCGCGCTTCGGGCTGACGGCGAGCGTCTGGACGCGGGACGCGGCGCGCGGGGAGGCGGTCGCACGGCGGCTCCGGGCGGGCGTCGTGACGGTGAACAACCACGCCTTCACCGGGGCCATCCCGGCGCTGCCCTGGGGCGGCGTCGGCGAGACGGGCTTCGGGGTGACGAACTCGCCGCACGCGCTCCACGCATTGGTGCGGCCGCGGGCCGTGGTCGTGGACGGCAACGCGCGGCCGGAGCTCTACTGGCACCCCTACGACGAGGCGCTCGAGCGGCTCGGGAAGGGCATGGCGGCGCTCCGCGGCAAGGGCGGGCCGATCACGAAGGTGCGCGCCGTGGCCAGGCTGCTCGGGGCGCTCCGCCGGCGCTTCTGA

1.3 (Optional) Gene group (e.g., head(`PGC_group`))

gene	gene_group	gene_label
bciE	bci	E
bchB	bch	B
bchC	bch	C
bchD	bch	D

1.4 (Optional) Candidate gene list (e.g., head(`photosynthesis_gene_list`))

bciE bchB bchC bchD bchE

2 Output Data Preview

2.1 Gene cluster information (`GC_meta`)

gene	qaccver	saccver	pident	length	mismatch	gapopen	qstart	qend	sstart	send	evalue	bitscore	genome	orf	contig	genome_contig	orf_position	gene_cluster	GC_orf_position	GC_present_length	GC_absent_length	GC_length	SeqName	Sequence	start	end	direction	gene_group	gene_label	Pgenome	Pstart	Pend	Pdirection
pufC	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_97	pufC_Rhodospirillum_centenum_RC1_2101_RCE	53.1	335	147	7	3	329	6	338	7.66E-112	333	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_97	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	97	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	1	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_97 # 117640 # 118917 # -1 # ID=85_97;partial=00;start_type=GTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.710	GTGAAGAAGATCGCCATCGCCTTCGTGAGCACCTGGCTCCTCATCGGGGCCGTCTACGCCTACGAGCCGACCGAGACCTCGCAGATCGGCGCCGACGGCGTCGCCATGCAGGTCACGCAGACCGAGGACGAGCTCGCCGCGCGCGTGGAGGCGAACACCGTCCCGCCGGCCATCCCGATGCCCCAGAGCAGCGGCGTGCTGGCGGCCGAGGAGTACGAGAACGTGCAGGTCCTCGGCCACCTCAACACGGCCCAGTTCACCCGGCTGATGACCTCCATCACGCTCTGGGTCGCGCCGGAGCAGGGCTGCGCCTACTGCCACAACACGAACAACCTGGCCTCCGACGAGCTCTACACGAAGCGCGTGGCGCGTCGGATGATCCAGATGACCTGGCACATCAACGAGAACTGGCAGTCGCACGTCCAGGAGACCGGCGTGACCTGCTACACGTGCCACCGCGGCAACAACGTGCCCCAGCACATCTGGTTCGAGACGCCGCCCGACGACCACGGCATGGTGGGCTGGCGTGGCTCGCAGAACGCCCCGAACGACCGGACGGGGATCAGCTCCCTGCCGAACGACGTGTTCGAGGTGTTCCTCGAGGAGGACGCGAGCATCCGGGTCCAGTCGGCCGGGGAGGCCTTCCCGAACGAGAACCGCGCGTCCATCAAGCAGGCCGAGTGGACCTATGGGCTGATGATGCACTTCTCCGAGTCGCTCGGGGTGAACTGCACGGCTTGCCACAACTCGCGCTCCTGGAACGACTGGAGCCAGAGCCCGGCCCGCCGCGGGACGGCCTGGCACGGCATCCGGATGGCGCGAAACCTCAACAACCACTGGCTGACGCCGCTGCGCGATCAGTTCCCGCCGAACCGGCTCGGCGAGCTGGGTGACGCCCCGAAGGCCAACTGCGCGACGTGCCACCAGGGCGCGTACCGCCCCCTGCTCGGGCACCGCATGCTCGAGGACTTCCCGTCCCTCGTACGGGCGATGCCGCAGCCCGAGATCGAGCCGGAGCCGGAGCCGGAGCCCGAGCTGGAAGGCGAGGGCGAGGCCGGCGGGCAGCTCGAGCCGGAGGGGGAGGCGCCCGCCGCCGAAGCCCCCGAGGGCACGAACGCTGCGCCGACGGCGATGGCTGCGCCGGCGGCGATGGCCGCTCCGACGGGGATGGCCGCGCCGGCGGCGATGGCTGCGCCGGCGGCGATGGCTGCTCCGGCGGTGGCCGAGCCGACGCCCATGGCCGCGCCGGCGGCGATGGCGGCCCCGGCACCGAACTGA	117640	118917	-1	puf	C	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	0	1277	FALSE
pufM	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_98	pufM_p_Myxococcota--c_Polyangia--o_Polyangiales--ERR1726576_bin.13---k141_102738_3	100	437	0	0	1	437	1	437	4.73E-308	834	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_98	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	98	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	2	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_98 # 118914 # 120224 # -1 # ID=85_98;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.704	ATGGCCCGCTACCAGAACATCTTCACGCAGATCCAAGTCGTCGGTCCGCCGGACACGCCGCCGCCGATCGACCCGGACTTCCGTACGAAGAAGACGCGCATGTCGCGGCTCCTCGGGTGGTTCGGCAACCCGCAGATCGGCCCCGTCTACCTGGGCTACACCGGCCTGGCGTCCGCGATCAGCTTCTTCATCGCTTTCGAGATCATCGGGCTCAACATGCTGGCCTCGGTGGACTGGGACGTCGTTCAGTTCATCCGCCAGCTCCCCTGGCTCGCGCTCGAACCGCCCCCGCCCTCTGCCGGGCTCTCCATCCCGACGCTTCAGGAGGGCGGCTGGTGGCTCATGGCCGGCTTCTTCCTCACGGCGTCGGTCATTCTCTGGTGGATTCGCACCTATCGGCGCGCACGCGCCCTGAAGATGGGCACGCACGTCGCGTGGGCCTTCGCCTCGGCGATCTGGCTCTACCTCGTCCTCGGCTTCATTCGCCCCTTGCTGATGGGGAGCTGGGGGGAGGCGGTGCCCTTCGGCATCTTCCCGCACCTCGACTGGACCGCCGCCTTCTCCGTTCGCTACGGCAACCTCTTCTACAACCCCTTCCACTGCCTCTCGATCGTCTTCCTCTACGGGTCGACGCTCCTCTTCGCCATGCACGGCGCGACGGTGCTCGCGCTCGGGCACGTGGGCGGTGAGCGTGAGGTGAGCCAGGTGGTCGACCGCGGCACGGCGGCCGAGCGCGGGGCGCTCTTCTGGCGCTGGACGATGGGCTTCAACGCGACCTTCGAGTCCATCCACCGCTGGGCCTGGTGGTTCGCGGTGCTCACGCCGCTCACCGGAGGCATCGGCATCCTCCTGACCGGCACCGCCGTCGACAACTGGTATCAGTGGGCCGTCGAGCACGACTTCGCGCCGGCCTATGAGGAGTCCTACGAGGTCGTCCCCGACCCGGTCGACGACCCGGCGAACGAGGACCTGCCCGGTATGCGCGGTGAGTCCACCGCGCAGTGGGAGCCGACCCCCTACGTGCCCGCCGAGGAGCCGGAGGCGCCCGAGGATGGTGCGGACGGCGCGGCCGCGGTCGAAGGCGTCGACGCCGAGGGCGGCGAGGATGCCGCCGCGGATCCCGCGAGCGAGGGCACGAGCGGCCAGCCGGAGACCGGCGCCGCGGCCCCGGAGAGCGAGCGCCTTCCGGACGAAGCGGCGGCGGCCGAGCCCGAAGGGGCTGCGCCGGAGCCCGAACCCCCCGCGCCGTCCGAGACGGCTGCCCCGAGCGAACCCGAGGCGCCCAGCGCGATGACCCCGGAGCAACCGTGA	118914	120224	-1	puf	M	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	1274	2584	FALSE
pufL	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_99	pufL_p_Myxococcota--c_Polyangia--o_Polyangiales--ERR1726567_bin.15---k141_184359_2	100	275	0	0	1	275	1	275	2.63E-214	583	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_99	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	99	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	3	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_99 # 120270 # 121094 # -1 # ID=85_99;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.648	ATGGGCCTACTGAGCTTCGAGCGGCGATATCGAGTCCGAGGAGGCACGCTCCTCGGGGGCGACCTATTCGATTTCTGGGTCGGGCCCTTCTACGTGGGGCTCTTCGGCGTCACGACGATCTTCTTCACGATCGTCGGCACCGCGCTGATCCTCTGGGAGGCCTCCCGGGGTGACACCTGGAACCCCTGGCTGATCAACATCCAGCCGCCTCCAATCGAGTACGGGCTCGCCTTCGCGCCCCTCGATCAGGGGGGCATCTGGCAGCTGGTCACCATCTGCGCCATCGGCGCCTTCGGATCCTGGGCGCTCCGACAGGCGGAGATCAGCCGCAAGCTCGGCATGGGCTACCACGTGCCCATCGCCTACGGCGTCGCGGTCTTCGCCTACGTCACGCTCGTGGTGATTCGCCCGGTGATGCTGGGCGCCTGGGGCCACGGCTTCCCCTACGGCATCTTCAGCCACCTCGATTGGGTGTCGAACGTCGGGTACCAGTACCTGCACTTCCACTACAACCCGGCCCACATGATCGCGGTGAGCTTCTTCTTCACCACGACGCTCGCGCTCTCCCTCCACGGCGGTTTGATCCTCTCCGCCGTGAATCCGCCGAAGGGAGAGAAGGTGAAGACCGCCGAGTACGAGGACGGGTTCTTCCGTGACCACATCGGCTACTCGATCGGCGCCCTGGGCATTCATCGACTCGGCCTCTTCCTGGCGCTGAGCGCCGGGATCTGGAGCGCGATCTGCATTCTCATCAGCGGCCCGATGTGGACCAAGGGGTGGCCCGAGTGGTGGGACTGGTGGCTCAACCTCCCCGTGTGGAGCTGA	120270	121094	-1	puf	L	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	2630	3454	FALSE
bchO	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_100	bchO_Pararhodospirillum_photometricum_RSPPHO_00117_RPM	44.9	265	144	1	33	295	28	292	6.97E-60	194	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_100	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	100	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	4	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_100 # 121191 # 122102 # -1 # ID=85_100;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.762	ATGAGCTCGGCCGTCGAAGAGCAGCGCGTCGAGCACCCGCGGGTCGAGCAGCAGCCCATCGAGCAGCAGCGCGTCGAGCACCAGCGCGTCGAGCGTTCGGGCGTGCGGTGGAACGTCGCCCGCCGCGGCGCCGGACCCACGCTCCTGGCGCTCCACGGGACCGGCAGCTCGAGCCGCTCCTTCTGCGCCCTCGCGGCCACGCTCGGTGCTCGCTTCACCGTCGTGGCGCCCGATCTACCCGGCCACGCCGGGAGCCGGATCGATCGCCGCTTCCGCCTCTCGCTCCCCTCGATCGCCGCCGCCCTCGGCGAGCTCATCGAGGCGCTCGCCGTCCAGCCGGCGCTGGTCCTCGCTCACTCCGCGGGCGCGGCGGTGGCGGCGCGCGCCATGCTCGACGGGGCTCTCCGCCCGGCGCTCTTCGTCGGGCTCGGCGCGGCCCTGACGCCCCTCGAGGGGCTCGCCCGGCTCGGCGCGCGCCCGGCGGCCGCGATGCTCGCCCGCTCGCCCATCACGCGGCGGGTGGCGCGCCGGGCTGGAGGCGCCCTCGTCGGACCGATCCTGCGCAGCGTCGGATCCACCGTCGGCCCCGAGGCCACACAGCGCTATCGGGAGCTCGCCCGCGATCCCGCCCACGTCGGGGCGGTCTTCTCGATGCTCGCCCAGTGGGATCTCGACGGGCTCCACGCGGCGCTACCACGCCTGGACGTACCGACCCTGCTCCTCGGCGGCGCCCGCGACGGCGCCACCCCGATCGCCCAGCAGCGCGCCCTCGCACGTCGCCTCCCGGCCGCGCGCGCGCACGTCGTCCTCGGCGCCGGGCACCTGCTCCACGAGGAGCGACCCGCCGAGATCGCGCGCCTCGTCGAGGCCGAGTGGAACAGATTGGACGGCGGTCGTGTCAAAAATGCTTGA	121191	122102	-1	bch	O	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	3551	4462	FALSE
bchD	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_101	bchD_p_Myxococcota--c_Polyangia--o_Polyangiales--GCA_002699025.1---PABA01000098.1_81	100	587	0	0	1	587	1	587	0	1064	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_101	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	101	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	5	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_101 # 122099 # 123859 # -1 # ID=85_101;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.792	ATGAGCGGCTGGCCCGACGTGGCGCGCGTCGCCGAGCTCCTGAGCGTCGACCCGGACGGCCTCGGAGGCGTGCGCCTGCGGGGTCGCCCGGGGCCGCACCGGCGCCGGGTGCTCGAGTGGGTGCGCGAGAGGCTGGCCCCGGAGGCGCCCTTCCGGCGCCTGCCCGCGCACGTGACCGAGGATCGGCTCCTCGGGGGCCTCGCGCTCGCGGAGACCTTGCGTTCGGGGCGGGCCGTCATGGAGCAGGGCGTGCTCGCGCGGAGCGACGGCGGCCTGCTCGTCGTGGCCATGGCCGAGCGGGCCGAGCGGGAGGTCGTGGCGCACCTCTGCGCGGCCCTCGACCGCGGCGCGATCACCGTCGAACGCGACGGCATGAGCGCCGAGGCGTCCTGCCGCGTGGGCCTCATCGCGCTCGACGAGGGCATCGACGAGGAGCACGTCGACCCGGCGCTCGCCGACCGGCTCGCCTTCGCGCTGGACCTCGACGCGCTCGATCCGCGGGGAGGGGCGGCGCCGGAACACGGACCCGAGGAGGTCGCGCGAGCCCGCGCCCGCCTCCCGCACGTGAGCCTCGGCGACGACATCATCGCGGCCCTCTCGGAGGCGGCCCAGGCCCTCGGCGTGGAGGCGCTCCGGCCGCTCCTGCTCGCGGCGAAGGCGGCCCGCGCGCACGCGGCGCTCCTCGGCCGGACCCGCGTCGAGGAGGAAGACGCCGGGATGGCGGCGCGCCTCGTCCTCGGCCCGAGGGCGACGCGAGCGCCGAGCGCCGAGCCCGAAGAGGCGGCCGAGCGCGAGGCCGAAGAGGGCGACCCCGACCCGGGAGGCGCCGGCGCGGCTGCAGCCGGCGAACGGGCGGACGGCGCCGACGAGGCCCCGCCGGGCGAGGTCCCGCTCGGCGATCTCGTCTTGGCGGCGGCCGAGAGCGGCATCCCGGCGGGGCTGCTCGACGCCCTCGACGTCGGGACCACCCGGCGGGCCGGCGCGACCGGTCGGAGCGGGGCGACGCGCATCGGCCCGAGCGGCGGCCGCCCGGCGGGGACGCGCGCCGCGCCGCCCACCCGAGGCCAGCGCCTGAACGTCGTCGAGACCCTCCGCGCCGCCGCGCCCTGGCAGCGGCTCCGCGGGGGCGGCTTCGGCGCGGGCGTGCGCGTCCGGCCGGAGGACTTCCGTGTCACCCGTCACCGGCAGCCGATCGAGAGCTGCGTGATCTTCGCCGTCGACGCGTCCGGCTCCGCCGCGCTTCGACGCCTGGCCGAGGCGAAGGGCGCCGTCGAGCGCGTGCTCGGCGACTGCTACGTGCGGCGCGACCACGTCGCCCTCGTCGCGTTCCGCCAGGACGGCGCCGAGCTGCTCCTGCCCCCGACGCGCTCCCTCGCCCGCGTGCGTCGCAGCCTGGCTGCCCTCGCCGGCGGCGGCGCGACCCCCCTCGCCGCGGGGATCGACGCCGCCCATCGGCTCGCCCTCGACGCCCGCGGGCGCGGCCGCGAGCCCATCGTGGTCGTCATGACCGACGGGCGGGCGAACGTGACCCGGGACGGCCGCCGGGACCCCGCGGTCGCCACCACGGACGCCCTCGAGAGCGCGCGCGGGCTCCAGCGAGCCGCCGTGCCGACCCTCTTCCTCGACACGGCCCCACGCCCCCGGCGCCGTGCCCGCGAGCTCGCCGAGGCCATGGACGCCCGCTACCTGCCGCTGCCCTACCTCGACGCGGCGGGGATCTCACGCCACGTCCAAGCGCTCGCCCGCGAGGGAGCCCGATGA	122099	123859	-1	bch	D	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	4459	6219	FALSE
bchI	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_102	bchI_p_Myxococcota--c_Polyangia--o_Polyangiales--GCA_002699025.1---PABA01000098.1_82	100	339	0	0	1	339	1	339	1.97E-239	652	Houyibacteriaceae--LLY-WYZ-15_3	k141_102864_102	k141_102864	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864	102	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	6	34	2	36	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864_102 # 123863 # 124879 # -1 # ID=85_102;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.745	ATGACGCCCTATCCCTTCACCGCCATCGTCGCGCAGGACGAGCTCAAGCTCGCCCTGCAGATCGCCACCGTCGACCGCAGCATCGGCGGGGTCCTCGCCTTCGGCGACCGCGGCACCGGCAAGTCGACCACCATCCGCGCGCTCGCCCGGCTCCTGCCGCCGATGCGCGTCGTCGCCAGCTGCCCGTACCACTGTGATCCGGCCGACGCGCGCGCTCGCTGTCCGCACTGTGCCGAAGCCGCAGGGGAGCGGGAGGCGATCGAGACGCCCGTGCCGGTCGTGGACCTGCCCCTCGGCGCCACCGAGGATCGCGTCGTCGGCGCGCTCGATCTCGAGGCGGCCCTCACGCGCGGGGAGCGCCGCTTCTCACCGGGCCTGCTCGCCGCGGCGCATCGAGGCTTCCTCTACATCGACGAGGTCAACCTCCTCCCCGATCACCTCGTGGATCTGCTGCTCGACGTCGCGGCCTCGGGCGAGAACGTGGTCGAGCGCGAGGGCCTGAGCGTGCGCCACCCCGCGCGCTTCGTGCTGATCGGCAGCGGAAACCCGGAGGAGGGCGAGCTGCGCCCCCAGCTGCTCGATCGCTTCGGCCTCTCGCTCGAGGTCCGCACGCCGGACGAGGTCGCGACGCGCGTCGAGGTCGTCAAGCGGCGCATGCGCTACGATCAGGACCCGGAGGCCTTCGCGGCCGCCTGGGCGGAGGACGAGGCGGCCCTCATCGTTCGCCTCCGGGACGCGCGGGCGCGCTTGCCCGAGGTGGCCGTCAGCGACGCCGTGATCGAGCGCGCGAGCCGGCTCTGCCAGGCGCTCGGCACCGACGGGCTCCGGGGGGAGCTGACCTTGATCCGCGCCGCGCGCGCGGCCGCCAGCCTCGACGCGCAGCGGGAGGTCGCCGACGTGCACCTCGCCCAGGTCGCCCCCCTCGCGCTCCGCCACCGGCTGCGACGCGCCCCCCTGGACGACGTCGGCTCGGGCGCGCGCGTGCAGAAGGCCGTCGAGGACGTGCTCGGGGGCTGA	123863	124879	-1	bch	I	Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1	6223	7239	FALSE

2.2 Gene cluster sequence (`GC_seq`)

>pufC_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
GTGAAGAAGATCGCCATCGCCTTCGTGAGCACCTGGCTCCTCATCGGGGCCGTCTACGCCTACGAGCCGACCGAGACCTCGCAGATCGGCGCCGACGGCGTCGCCATGCAGGTCACGCAGACCGAGGACGAGCTCGCCGCGCGCGTGGAGGCGAACACCGTCCCGCCGGCCATCCCGATGCCCCAGAGCAGCGGCGTGCTGGCGGCCGAGGAGTACGAGAACGTGCAGGTCCTCGGCCACCTCAACACGGCCCAGTTCACCCGGCTGATGACCTCCATCACGCTCTGGGTCGCGCCGGAGCAGGGCTGCGCCTACTGCCACAACACGAACAACCTGGCCTCCGACGAGCTCTACACGAAGCGCGTGGCGCGTCGGATGATCCAGATGACCTGGCACATCAACGAGAACTGGCAGTCGCACGTCCAGGAGACCGGCGTGACCTGCTACACGTGCCACCGCGGCAACAACGTGCCCCAGCACATCTGGTTCGAGACGCCGCCCGACGACCACGGCATGGTGGGCTGGCGTGGCTCGCAGAACGCCCCGAACGACCGGACGGGGATCAGCTCCCTGCCGAACGACGTGTTCGAGGTGTTCCTCGAGGAGGACGCGAGCATCCGGGTCCAGTCGGCCGGGGAGGCCTTCCCGAACGAGAACCGCGCGTCCATCAAGCAGGCCGAGTGGACCTATGGGCTGATGATGCACTTCTCCGAGTCGCTCGGGGTGAACTGCACGGCTTGCCACAACTCGCGCTCCTGGAACGACTGGAGCCAGAGCCCGGCCCGCCGCGGGACGGCCTGGCACGGCATCCGGATGGCGCGAAACCTCAACAACCACTGGCTGACGCCGCTGCGCGATCAGTTCCCGCCGAACCGGCTCGGCGAGCTGGGTGACGCCCCGAAGGCCAACTGCGCGACGTGCCACCAGGGCGCGTACCGCCCCCTGCTCGGGCACCGCATGCTCGAGGACTTCCCGTCCCTCGTACGGGCGATGCCGCAGCCCGAGATCGAGCCGGAGCCGGAGCCGGAGCCCGAGCTGGAAGGCGAGGGCGAGGCCGGCGGGCAGCTCGAGCCGGAGGGGGAGGCGCCCGCCGCCGAAGCCCCCGAGGGCACGAACGCTGCGCCGACGGCGATGGCTGCGCCGGCGGCGATGGCCGCTCCGACGGGGATGGCCGCGCCGGCGGCGATGGCTGCGCCGGCGGCGATGGCTGCTCCGGCGGTGGCCGAGCCGACGCCCATGGCCGCGCCGGCGGCGATGGCGGCCCCGGCACCGAACTGA
>pufM_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGGCCCGCTACCAGAACATCTTCACGCAGATCCAAGTCGTCGGTCCGCCGGACACGCCGCCGCCGATCGACCCGGACTTCCGTACGAAGAAGACGCGCATGTCGCGGCTCCTCGGGTGGTTCGGCAACCCGCAGATCGGCCCCGTCTACCTGGGCTACACCGGCCTGGCGTCCGCGATCAGCTTCTTCATCGCTTTCGAGATCATCGGGCTCAACATGCTGGCCTCGGTGGACTGGGACGTCGTTCAGTTCATCCGCCAGCTCCCCTGGCTCGCGCTCGAACCGCCCCCGCCCTCTGCCGGGCTCTCCATCCCGACGCTTCAGGAGGGCGGCTGGTGGCTCATGGCCGGCTTCTTCCTCACGGCGTCGGTCATTCTCTGGTGGATTCGCACCTATCGGCGCGCACGCGCCCTGAAGATGGGCACGCACGTCGCGTGGGCCTTCGCCTCGGCGATCTGGCTCTACCTCGTCCTCGGCTTCATTCGCCCCTTGCTGATGGGGAGCTGGGGGGAGGCGGTGCCCTTCGGCATCTTCCCGCACCTCGACTGGACCGCCGCCTTCTCCGTTCGCTACGGCAACCTCTTCTACAACCCCTTCCACTGCCTCTCGATCGTCTTCCTCTACGGGTCGACGCTCCTCTTCGCCATGCACGGCGCGACGGTGCTCGCGCTCGGGCACGTGGGCGGTGAGCGTGAGGTGAGCCAGGTGGTCGACCGCGGCACGGCGGCCGAGCGCGGGGCGCTCTTCTGGCGCTGGACGATGGGCTTCAACGCGACCTTCGAGTCCATCCACCGCTGGGCCTGGTGGTTCGCGGTGCTCACGCCGCTCACCGGAGGCATCGGCATCCTCCTGACCGGCACCGCCGTCGACAACTGGTATCAGTGGGCCGTCGAGCACGACTTCGCGCCGGCCTATGAGGAGTCCTACGAGGTCGTCCCCGACCCGGTCGACGACCCGGCGAACGAGGACCTGCCCGGTATGCGCGGTGAGTCCACCGCGCAGTGGGAGCCGACCCCCTACGTGCCCGCCGAGGAGCCGGAGGCGCCCGAGGATGGTGCGGACGGCGCGGCCGCGGTCGAAGGCGTCGACGCCGAGGGCGGCGAGGATGCCGCCGCGGATCCCGCGAGCGAGGGCACGAGCGGCCAGCCGGAGACCGGCGCCGCGGCCCCGGAGAGCGAGCGCCTTCCGGACGAAGCGGCGGCGGCCGAGCCCGAAGGGGCTGCGCCGGAGCCCGAACCCCCCGCGCCGTCCGAGACGGCTGCCCCGAGCGAACCCGAGGCGCCCAGCGCGATGACCCCGGAGCAACCGTGA
>pufL_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGGGCCTACTGAGCTTCGAGCGGCGATATCGAGTCCGAGGAGGCACGCTCCTCGGGGGCGACCTATTCGATTTCTGGGTCGGGCCCTTCTACGTGGGGCTCTTCGGCGTCACGACGATCTTCTTCACGATCGTCGGCACCGCGCTGATCCTCTGGGAGGCCTCCCGGGGTGACACCTGGAACCCCTGGCTGATCAACATCCAGCCGCCTCCAATCGAGTACGGGCTCGCCTTCGCGCCCCTCGATCAGGGGGGCATCTGGCAGCTGGTCACCATCTGCGCCATCGGCGCCTTCGGATCCTGGGCGCTCCGACAGGCGGAGATCAGCCGCAAGCTCGGCATGGGCTACCACGTGCCCATCGCCTACGGCGTCGCGGTCTTCGCCTACGTCACGCTCGTGGTGATTCGCCCGGTGATGCTGGGCGCCTGGGGCCACGGCTTCCCCTACGGCATCTTCAGCCACCTCGATTGGGTGTCGAACGTCGGGTACCAGTACCTGCACTTCCACTACAACCCGGCCCACATGATCGCGGTGAGCTTCTTCTTCACCACGACGCTCGCGCTCTCCCTCCACGGCGGTTTGATCCTCTCCGCCGTGAATCCGCCGAAGGGAGAGAAGGTGAAGACCGCCGAGTACGAGGACGGGTTCTTCCGTGACCACATCGGCTACTCGATCGGCGCCCTGGGCATTCATCGACTCGGCCTCTTCCTGGCGCTGAGCGCCGGGATCTGGAGCGCGATCTGCATTCTCATCAGCGGCCCGATGTGGACCAAGGGGTGGCCCGAGTGGTGGGACTGGTGGCTCAACCTCCCCGTGTGGAGCTGA
>bchO_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGAGCTCGGCCGTCGAAGAGCAGCGCGTCGAGCACCCGCGGGTCGAGCAGCAGCCCATCGAGCAGCAGCGCGTCGAGCACCAGCGCGTCGAGCGTTCGGGCGTGCGGTGGAACGTCGCCCGCCGCGGCGCCGGACCCACGCTCCTGGCGCTCCACGGGACCGGCAGCTCGAGCCGCTCCTTCTGCGCCCTCGCGGCCACGCTCGGTGCTCGCTTCACCGTCGTGGCGCCCGATCTACCCGGCCACGCCGGGAGCCGGATCGATCGCCGCTTCCGCCTCTCGCTCCCCTCGATCGCCGCCGCCCTCGGCGAGCTCATCGAGGCGCTCGCCGTCCAGCCGGCGCTGGTCCTCGCTCACTCCGCGGGCGCGGCGGTGGCGGCGCGCGCCATGCTCGACGGGGCTCTCCGCCCGGCGCTCTTCGTCGGGCTCGGCGCGGCCCTGACGCCCCTCGAGGGGCTCGCCCGGCTCGGCGCGCGCCCGGCGGCCGCGATGCTCGCCCGCTCGCCCATCACGCGGCGGGTGGCGCGCCGGGCTGGAGGCGCCCTCGTCGGACCGATCCTGCGCAGCGTCGGATCCACCGTCGGCCCCGAGGCCACACAGCGCTATCGGGAGCTCGCCCGCGATCCCGCCCACGTCGGGGCGGTCTTCTCGATGCTCGCCCAGTGGGATCTCGACGGGCTCCACGCGGCGCTACCACGCCTGGACGTACCGACCCTGCTCCTCGGCGGCGCCCGCGACGGCGCCACCCCGATCGCCCAGCAGCGCGCCCTCGCACGTCGCCTCCCGGCCGCGCGCGCGCACGTCGTCCTCGGCGCCGGGCACCTGCTCCACGAGGAGCGACCCGCCGAGATCGCGCGCCTCGTCGAGGCCGAGTGGAACAGATTGGACGGCGGTCGTGTCAAAAATGCTTGA
>bchD_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGAGCGGCTGGCCCGACGTGGCGCGCGTCGCCGAGCTCCTGAGCGTCGACCCGGACGGCCTCGGAGGCGTGCGCCTGCGGGGTCGCCCGGGGCCGCACCGGCGCCGGGTGCTCGAGTGGGTGCGCGAGAGGCTGGCCCCGGAGGCGCCCTTCCGGCGCCTGCCCGCGCACGTGACCGAGGATCGGCTCCTCGGGGGCCTCGCGCTCGCGGAGACCTTGCGTTCGGGGCGGGCCGTCATGGAGCAGGGCGTGCTCGCGCGGAGCGACGGCGGCCTGCTCGTCGTGGCCATGGCCGAGCGGGCCGAGCGGGAGGTCGTGGCGCACCTCTGCGCGGCCCTCGACCGCGGCGCGATCACCGTCGAACGCGACGGCATGAGCGCCGAGGCGTCCTGCCGCGTGGGCCTCATCGCGCTCGACGAGGGCATCGACGAGGAGCACGTCGACCCGGCGCTCGCCGACCGGCTCGCCTTCGCGCTGGACCTCGACGCGCTCGATCCGCGGGGAGGGGCGGCGCCGGAACACGGACCCGAGGAGGTCGCGCGAGCCCGCGCCCGCCTCCCGCACGTGAGCCTCGGCGACGACATCATCGCGGCCCTCTCGGAGGCGGCCCAGGCCCTCGGCGTGGAGGCGCTCCGGCCGCTCCTGCTCGCGGCGAAGGCGGCCCGCGCGCACGCGGCGCTCCTCGGCCGGACCCGCGTCGAGGAGGAAGACGCCGGGATGGCGGCGCGCCTCGTCCTCGGCCCGAGGGCGACGCGAGCGCCGAGCGCCGAGCCCGAAGAGGCGGCCGAGCGCGAGGCCGAAGAGGGCGACCCCGACCCGGGAGGCGCCGGCGCGGCTGCAGCCGGCGAACGGGCGGACGGCGCCGACGAGGCCCCGCCGGGCGAGGTCCCGCTCGGCGATCTCGTCTTGGCGGCGGCCGAGAGCGGCATCCCGGCGGGGCTGCTCGACGCCCTCGACGTCGGGACCACCCGGCGGGCCGGCGCGACCGGTCGGAGCGGGGCGACGCGCATCGGCCCGAGCGGCGGCCGCCCGGCGGGGACGCGCGCCGCGCCGCCCACCCGAGGCCAGCGCCTGAACGTCGTCGAGACCCTCCGCGCCGCCGCGCCCTGGCAGCGGCTCCGCGGGGGCGGCTTCGGCGCGGGCGTGCGCGTCCGGCCGGAGGACTTCCGTGTCACCCGTCACCGGCAGCCGATCGAGAGCTGCGTGATCTTCGCCGTCGACGCGTCCGGCTCCGCCGCGCTTCGACGCCTGGCCGAGGCGAAGGGCGCCGTCGAGCGCGTGCTCGGCGACTGCTACGTGCGGCGCGACCACGTCGCCCTCGTCGCGTTCCGCCAGGACGGCGCCGAGCTGCTCCTGCCCCCGACGCGCTCCCTCGCCCGCGTGCGTCGCAGCCTGGCTGCCCTCGCCGGCGGCGGCGCGACCCCCCTCGCCGCGGGGATCGACGCCGCCCATCGGCTCGCCCTCGACGCCCGCGGGCGCGGCCGCGAGCCCATCGTGGTCGTCATGACCGACGGGCGGGCGAACGTGACCCGGGACGGCCGCCGGGACCCCGCGGTCGCCACCACGGACGCCCTCGAGAGCGCGCGCGGGCTCCAGCGAGCCGCCGTGCCGACCCTCTTCCTCGACACGGCCCCACGCCCCCGGCGCCGTGCCCGCGAGCTCGCCGAGGCCATGGACGCCCGCTACCTGCCGCTGCCCTACCTCGACGCGGCGGGGATCTCACGCCACGTCCAAGCGCTCGCCCGCGAGGGAGCCCGATGA
>bchI_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGACGCCCTATCCCTTCACCGCCATCGTCGCGCAGGACGAGCTCAAGCTCGCCCTGCAGATCGCCACCGTCGACCGCAGCATCGGCGGGGTCCTCGCCTTCGGCGACCGCGGCACCGGCAAGTCGACCACCATCCGCGCGCTCGCCCGGCTCCTGCCGCCGATGCGCGTCGTCGCCAGCTGCCCGTACCACTGTGATCCGGCCGACGCGCGCGCTCGCTGTCCGCACTGTGCCGAAGCCGCAGGGGAGCGGGAGGCGATCGAGACGCCCGTGCCGGTCGTGGACCTGCCCCTCGGCGCCACCGAGGATCGCGTCGTCGGCGCGCTCGATCTCGAGGCGGCCCTCACGCGCGGGGAGCGCCGCTTCTCACCGGGCCTGCTCGCCGCGGCGCATCGAGGCTTCCTCTACATCGACGAGGTCAACCTCCTCCCCGATCACCTCGTGGATCTGCTGCTCGACGTCGCGGCCTCGGGCGAGAACGTGGTCGAGCGCGAGGGCCTGAGCGTGCGCCACCCCGCGCGCTTCGTGCTGATCGGCAGCGGAAACCCGGAGGAGGGCGAGCTGCGCCCCCAGCTGCTCGATCGCTTCGGCCTCTCGCTCGAGGTCCGCACGCCGGACGAGGTCGCGACGCGCGTCGAGGTCGTCAAGCGGCGCATGCGCTACGATCAGGACCCGGAGGCCTTCGCGGCCGCCTGGGCGGAGGACGAGGCGGCCCTCATCGTTCGCCTCCGGGACGCGCGGGCGCGCTTGCCCGAGGTGGCCGTCAGCGACGCCGTGATCGAGCGCGCGAGCCGGCTCTGCCAGGCGCTCGGCACCGACGGGCTCCGGGGGGAGCTGACCTTGATCCGCGCCGCGCGCGCGGCCGCCAGCCTCGACGCGCAGCGGGAGGTCGCCGACGTGCACCTCGCCCAGGTCGCCCCCCTCGCGCTCCGCCACCGGCTGCGACGCGCCCCCCTGGACGACGTCGGCTCGGGCGCGCGCGTGCAGAAGGCCGTCGAGGACGTGCTCGGGGGCTGA

2.3 Gene cluster plot (`GC_plot`)

Case 2: Using eggNOG (evolutionary gene genealogy Nonsupervised Orthologous Groups) format result

# Case 2: Using eggNOG result with Full pipeline (Find Cluster + Extract FASTA + Plot Cluster)
library(gclink)
data(eggnog_df)
data(seq_data)
data(KO_group)
KOs = c("K02291","K09844","K20611","K13789",
        "K09846","K08926","K08927","K08928",
        "K08929","K13991","K04035","K04039",
        "K11337","K03404","K11336","K04040",
        "K03403","K03405","K04037","K03428",
        "K04038","K06049","K10960","K11333",
        "K11334","K11335","K08226","K08226",
        "K09773")
rename_KOs = paste0("ko:", KOs)
eggnog_df$qaccver = eggnog_df$`#query`
eggnog_df$saccver = eggnog_df$KEGG_ko
eggnog_df$evalue = eggnog_df$evalue
eggnog_df$bitscore = eggnog_df$score
eggnog_df$gene = eggnog_df$KEGG_ko
gc_list_2 = gclink(in_blastp_df = eggnog_df,
                  in_seq_data = seq_data,
                  in_gene_list = rename_KOs,
                  in_GC_group  = KO_group,
                  AllGeneNum = 50,
                  MinConSeq  = 25,
                  apply_evalue_filter = FALSE,
                  min_evalue = 1,
                  apply_score_filter = TRUE,
                  min_score = 10,
                  orf_before_first = 1,
                  orf_after_last = 1,
                  levels_gene_group = c('bch','puh','puf','crt',
                                        'acsF','assembly','hypothetical ORF'),
                  color_theme = c('#3BAA51','#6495ED','#DD2421','#EF9320',
                                  '#F8EB00','#FF0683','grey'))
gc_meta_2 = gc_list_2[["GC_meta"]]
gc_seq_2 = gc_list_2[["GC_seq"]]
gc_plot_2 = gc_list_2[["GC_plot"]]
head(gc_meta_2)   # Cluster metadata
head(gc_seq_2)    # FASTA sequences
print(gc_plot_2)  # Visualization

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output from eggNOG (e.g., head(`eggnog_df`))

#query	seed_ortholog	evalue	score	eggNOG_OGs	max_annot_lvl	COG_category	Description	Preferred_name	GOs	EC	KEGG_ko	KEGG_Pathway	KEGG_Module	KEGG_Reaction	KEGG_rclass	BRITE	KEGG_TC	CAZy	BiGG_Reaction	PFAMs
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_1	439375.Oant_2732	1.57E-45	162	COG3293@1\|root,COG3293@2\|Bacteria,1PVIT@1224\|Proteobacteria,2TURP@28211\|Alphaproteobacteria,1J3RT@118882\|Brucellaceae	28211\|Alphaproteobacteria	L	Transposase DDE domain	-	-	-	ko:K07492	-	-	-	-	ko00000	-	-	-	DDE_Tnp_1,DDE_Tnp_1_2,DUF4096
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_2	1173264.KI913949_gene2450	3.58E-17	83.6	COG3335@1\|root,COG3415@1\|root,COG3335@2\|Bacteria,COG3415@2\|Bacteria,1G39S@1117\|Cyanobacteria,1HCKE@1150\|Oscillatoriales	1117\|Cyanobacteria	L	COGs COG3415 Transposase and inactivated derivatives	-	-	-	ko:K07494	-	-	-	-	ko00000	-	-	-	DDE_3,HTH_32,HTH_Tnp_IS630
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_3	794903.OPIT5_03400	3.03E-30	114	COG3335@1\|root,COG3335@2\|Bacteria	2\|Bacteria	L	DDE superfamily endonuclease	-	-	-	ko:K07494	-	-	-	-	ko00000	-	-	-	DDE_3,HTH_Tnp_IS630
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_5	502025.Hoch_2790	2.78E-50	191	2AY84@1\|root,31QA9@2\|Bacteria,1QMYF@1224\|Proteobacteria,4374U@68525\|delta/epsilon subdivisions,2X20E@28221\|Deltaproteobacteria,2YWTZ@29\|Myxococcales	28221\|Deltaproteobacteria	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_11	105420.BBPO01000003_gene1121	2.00E-11	72.8	COG2887@1\|root,COG2887@2\|Bacteria,2GJC5@201174\|Actinobacteria,2NGJC@228398\|Streptacidiphilus	201174\|Actinobacteria	L	Protein of unknown function (DUF2800)	recB	-	-	ko:K07465	-	-	-	-	ko00000	-	-	-	PDDEXK_1
Kuafuiibacteriaceae--GCA_016703535.1---JADJBV010000001.1_12	1122915.AUGY01000071_gene4398	2.13E-37	152	COG1201@1\|root,COG1201@2\|Bacteria,1UHYQ@1239\|Firmicutes,4ISB0@91061\|Bacilli,277Q5@186822\|Paenibacillaceae	91061\|Bacilli	L	helicase superfamily c-terminal domain	-	-	-	-	-	-	-	-	-	-	-	-	DUF1998,Helicase_C

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

Same with Case 1

1.3 (Optional) KO/gene group (e.g., head(`KO_group`))

gene	gene_group	gene_label
ko:K04035	acsF	acsF
ko:K08226	assembly	bch2
ko:K04039	bch	B
ko:K11337	bch	C
ko:K03404	bch	D
ko:K11336	bch	F

1.4 (Optional) Candidate KO/gene list

ko:K04035 ko:K08226 ko:K04039 ko:K11337 ko:K03404 ko:K11336

2 Output Data Preview

2.1 Gene cluster information (`GC_meta`)

Similar with Case 1

2.2 Gene cluster sequence (`GC_seq`)

Similar with Case 1

2.3 Gene cluster plot (`GC_plot`)

Documentation

Full function reference:

?gclink::gclink

Citation

If you use gclink in your research, please cite:

Li, L., Huang, D., Hu, Y., Rudling, N. M., Canniffe, D. P., Wang, F., & Wang, Y. "Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle." Nature Communications (2023), 14, 6450. https://doi.org/10.1038/s41467-023-42193-7

Dependencies

R (≥ 3.5)
dplyr (≥ 1.1.4)
gggenes (≥ 0.5.1)
ggplot2 (≥ 3.5.2)

License

Contact

Maintainer: Liuyang Li [email protected]
Bug reports: https://github.com/LiuyangLee/gclink/issues.

r-gclink

gclink: Gene-Cluster Discovery, Annotation and Visualization

Overview

Key Features

Adaptive Workflow

Cluster Detection

Visualization

Installation

Case 1: Using blastp result

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output (e.g., head(`blastp_df`))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

1.3 (Optional) Gene group (e.g., head(`PGC_group`))

1.4 (Optional) Candidate gene list (e.g., head(`photosynthesis_gene_list`))

2 Output Data Preview

2.1 Gene cluster information (`GC_meta`)

2.2 Gene cluster sequence (`GC_seq`)

2.3 Gene cluster plot (`GC_plot`)

Case 2: Using eggNOG (evolutionary gene genealogy Nonsupervised Orthologous Groups) format result

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output from eggNOG (e.g., head(`eggnog_df`))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

1.3 (Optional) KO/gene group (e.g., head(`KO_group`))

1.4 (Optional) Candidate KO/gene list

2 Output Data Preview

2.1 Gene cluster information (`GC_meta`)

2.2 Gene cluster sequence (`GC_seq`)

2.3 Gene cluster plot (`GC_plot`)

Documentation

Citation

Dependencies

License

Contact

Version

License

Status

Source

Homepage

Platforms (76)

gclink: Gene-Cluster Discovery, Annotation and Visualization

Overview

Key Features

Adaptive Workflow

Cluster Detection

Visualization

Installation

Case 1: Using blastp result

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output (e.g., head(blastp_df))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(seq_data))

1.3 (Optional) Gene group (e.g., head(PGC_group))

1.4 (Optional) Candidate gene list (e.g., head(photosynthesis_gene_list))

2 Output Data Preview

2.1 Gene cluster information (GC_meta)

2.2 Gene cluster sequence (GC_seq)

2.3 Gene cluster plot (GC_plot)

Case 2: Using eggNOG (evolutionary gene genealogy Nonsupervised Orthologous Groups) format result

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output from eggNOG (e.g., head(eggnog_df))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(seq_data))

1.3 (Optional) KO/gene group (e.g., head(KO_group))

1.4 (Optional) Candidate KO/gene list

2 Output Data Preview

2.1 Gene cluster information (GC_meta)

2.2 Gene cluster sequence (GC_seq)

2.3 Gene cluster plot (GC_plot)

Documentation

Citation

Dependencies

License

Contact

Version

License

Status

Source

Homepage

Platforms76 (76)

1.1 A dataframe of Diamond BLASTp output (e.g., head(`blastp_df`))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

1.3 (Optional) Gene group (e.g., head(`PGC_group`))

1.4 (Optional) Candidate gene list (e.g., head(`photosynthesis_gene_list`))

2.1 Gene cluster information (`GC_meta`)

2.2 Gene cluster sequence (`GC_seq`)

2.3 Gene cluster plot (`GC_plot`)

1.1 A dataframe of Diamond BLASTp output from eggNOG (e.g., head(`eggnog_df`))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(`seq_data`))

1.3 (Optional) KO/gene group (e.g., head(`KO_group`))

2.1 Gene cluster information (`GC_meta`)

2.2 Gene cluster sequence (`GC_seq`)

2.3 Gene cluster plot (`GC_plot`)

Platforms (76)