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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))

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))

bciE bchB bchC bchD bchE

2 Output Data Preview

2.1 Gene cluster information (GC_meta)

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))

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))

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

GPL-3 © Liuyang Li

Contact

• Maintainer: Liuyang Li cyanobacteria@yeah.net
• Bug reports: https://github.com/LiuyangLee/gclink/issues

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.