Category	Resource ID	Resource name	Used version or status	Website application	Use relationship	Official URL	Source-code URL	Software download URL	Model download URL	Reference ID	Paper title	Publication year	DOI	Paper URL	Paper relationship	Limitations
Software or website algorithm	LocPro	LocPro	Offline bundle; upstream semantic version not recorded	Direct localization predictions for representative OH-1004 and TK1151 proteins using ESM2 and PROFEAT features	Used by the website or supplied as a component	https://idrblab.org/LocPro/	https://github.com/idrblab/LocPro	https://drive.google.com/drive/folders/1twlsmrQRBF7gFMG97tnH0HxzjvExyfsA	https://drive.google.com/drive/folders/1twlsmrQRBF7gFMG97tnH0HxzjvExyfsA	REF014	LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research	2025	10.1016/j.jpha.2025.101255	https://doi.org/10.1016/j.jpha.2025.101255	Software methods publication	Computational prediction; no microscopy or experimental localization claimed
Software or website algorithm	ESM2	ESM2	LocPro-bundled model; checkpoint revision not recorded	Protein language-model features for LocPro	Used by the website or supplied as a component	https://github.com/facebookresearch/esm	https://github.com/facebookresearch/esm	https://github.com/facebookresearch/esm		REF015	Evolutionary-scale prediction of atomic-level protein structure with a language model	2023	10.1126/science.ade2574	https://doi.org/10.1126/science.ade2574	Software methods publication	LocPro component, rather than a standalone localization predictor
Software or website algorithm	PROFEAT (sequence features; LocPro reference)	PROFEAT (sequence features; LocPro reference)	Feature implementation in the LocPro offline bundle; standalone version not recorded	Sequence physicochemical features for LocPro	Used by the website or supplied as a component	https://doi.org/10.1093/nar/gkr284				REF016	Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence	2011	10.1093/nar/gkr284	https://doi.org/10.1093/nar/gkr284	Software methods publication	Publication and official software source verified; distinct from similarly named network-feature tools
Software or website algorithm	HISAT2	HISAT2	2.2.1	RNA-seq alignment to the TK1151 reference	Used by the website or supplied as a component	https://daehwankimlab.github.io/hisat2/	https://github.com/DaehwanKimLab/hisat2/releases	https://github.com/DaehwanKimLab/hisat2/releases		REF017	Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype	2019	10.1038/s41587-019-0201-4	https://doi.org/10.1038/s41587-019-0201-4	Software methods publication	Installed executable version verified; parameters based on retained scripts
Software or website algorithm	StringTie	StringTie	3.0.3	Fixed-model re-quantification of 109 samples using -e -G; coverage, FPKM and TPM	Used by the website or supplied as a component	https://ccb.jhu.edu/software/stringtie/	https://github.com/gpertea/stringtie/releases	https://github.com/gpertea/stringtie/releases		REF018	StringTie enables improved reconstruction of a transcriptome from RNA-seq reads	2015	10.1038/nbt.3122	https://doi.org/10.1038/nbt.3122	Software methods publication	Not featureCounts integer counts; 98,473 TKU-model genes
Software or website algorithm	SAMtools	SAMtools	RNA pipeline: 1.13; variant pipeline: 1.20	BAM/CRAM processing, sorting and indexing	Used by the website or supplied as a component	https://www.htslib.org/	https://github.com/samtools/samtools/releases	https://github.com/samtools/samtools/releases		REF019	Twelve years of SAMtools and BCFtools	2021	10.1093/gigascience/giab008	https://doi.org/10.1093/gigascience/giab008	Software methods publication	The two execution environments are recorded separately
Software or website algorithm	SRA Toolkit	SRA Toolkit	3.4.1	Retrieval of public SRA reads with fasterq-dump	Used by the website or supplied as a component	https://github.com/ncbi/sra-tools	https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit	https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Actual retained archive-download paths preserved
Software or website algorithm	BLAST+	BLAST+	2.12.0+	Public BLAST searches, historical-ID sequence mapping and homology alignment	Used by the website or supplied as a component	https://blast.ncbi.nlm.nih.gov/	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/		REF020	BLAST+: architecture and applications	2009	10.1186/1471-2105-10-421	https://doi.org/10.1186/1471-2105-10-421	Software methods publication	Short-sequence alignment parameters controlled by the website
Software or website algorithm	HMMER	HMMER	3.3.2	Pfam-A protein-domain scanning	Used by the website or supplied as a component	https://hmmer.org/	https://hmmer.org/download.html	https://hmmer.org/download.html		REF021	Accelerated Profile HMM Searches	2011	10.1371/journal.pcbi.1002195	https://doi.org/10.1371/journal.pcbi.1002195	Software methods publication	Domain hits constitute computational evidence
Software or website algorithm	FIMO	FIMO	5.4.1	Retained PlantTFDB/JASPAR motif scans of promoters	Used by the website or supplied as a component	https://meme-suite.org/meme/doc/fimo.html	https://meme-suite.org/meme/doc/download.html	https://meme-suite.org/meme/doc/download.html		REF022	FIMO: scanning for occurrences of a given motif	2011	10.1093/bioinformatics/btr064	https://doi.org/10.1093/bioinformatics/btr064	Software methods publication	Cached scans use 2500-bp promoters; current on-demand 4000-bp scans use the site-developed implementation
Software or website algorithm	DIAMOND	DIAMOND	2.2.4	Protein homology, reference-version mapping and Swiss-Prot annotation transfer	Used by the website or supplied as a component	https://github.com/bbuchfink/diamond	https://github.com/bbuchfink/diamond/releases	https://github.com/bbuchfink/diamond/releases		REF023	Sensitive protein alignments at tree-of-life scale using DIAMOND	2021	10.1038/s41592-021-01101-x	https://doi.org/10.1038/s41592-021-01101-x	Software methods publication	Homology-based annotation does not establish experimental validation
Software or website algorithm	JCVI	JCVI	1.6.6	Synteny and ortholog blocks between TK1151 and OH-1004	Used by the website or supplied as a component	https://github.com/tanghaibao/jcvi	https://pypi.org/project/jcvi/	https://pypi.org/project/jcvi/		REF024	JCVI: A versatile toolkit for comparative genomics analysis	2024	10.1002/imt2.211	https://doi.org/10.1002/imt2.211	Software methods publication	Retained methods: -cscore 0.70 and diamond_blastp
Software or website algorithm	minimap2	minimap2	2.30-r1287	Short-read realignment of CRA009020 using -ax sr --secondary=no	Used by the website or supplied as a component	https://github.com/lh3/minimap2	https://github.com/lh3/minimap2/releases	https://github.com/lh3/minimap2/releases		REF025	Minimap2: pairwise alignment for nucleotide sequences	2018	10.1093/bioinformatics/bty191	https://doi.org/10.1093/bioinformatics/bty191	Software methods publication	Actual use of this tool verified; obsolete BWA preparation directories are not treated as the executed method
Software or website algorithm	bcftools	bcftools	1.20	Variant mpileup, calling and filtering	Used by the website or supplied as a component	https://www.htslib.org/	https://github.com/samtools/bcftools/releases	https://github.com/samtools/bcftools/releases		REF019	Twelve years of SAMtools and BCFtools	2021	10.1093/gigascience/giab008	https://doi.org/10.1093/gigascience/giab008	Software methods publication	Diploid assumption; QUAL>=30, DP>=10 and MQ/BQ>=20
Software or website algorithm	KMC3	KMC3	3.2.1	Resequencing k-mer counting	Used by the website or supplied as a component	https://github.com/refresh-bio/KMC	https://github.com/refresh-bio/KMC/releases	https://github.com/refresh-bio/KMC/releases		REF026	KMC 3: counting and manipulating k-mer statistics	2017	10.1093/bioinformatics/btx304	https://doi.org/10.1093/bioinformatics/btx304	Software methods publication	Installed executable version verified
Software or website algorithm	MaxQuant (upstream source analysis)	MaxQuant (upstream source analysis)	Author-processed outputs retained by the website; version unconfirmed	Upstream proteomic processing of PXD011773 by the original authors	Used by the upstream authors	https://www.maxquant.org/maxquant/	https://www.maxquant.org/archive/maxquant	https://www.maxquant.org/archive/maxquant		REF027	MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification	2008	10.1038/nbt.1511	https://doi.org/10.1038/nbt.1511	Software methods publication	Used by upstream authors; the website imports results and does not claim reanalysis of raw mass-spectrometry data
Software or website algorithm	featureCounts	featureCounts	2.0.3	Retained independent integer-count data from nine MeJA samples and historical coexpression input	Used by the website or supplied as a component	https://subread.sourceforge.net/	https://sourceforge.net/projects/subread/files/	https://sourceforge.net/projects/subread/files/		REF028	featureCounts: an efficient general purpose program for assigning sequence reads to genomic features	2014	10.1093/bioinformatics/btt656	https://doi.org/10.1093/bioinformatics/btt656	Software methods publication	Does not justify describing uniform-v4 coverage as integer counts
Software or website algorithm	JBrowse 2	JBrowse 2	Major version 2; exact installed build not documented	Genome browser and source-model tracks	Used by the website or supplied as a component	https://jbrowse.org/jb2/	https://github.com/GMOD/jbrowse-components/releases	https://github.com/GMOD/jbrowse-components/releases		REF029	JBrowse 2: a modular genome browser with views of synteny and structural variation	2023	10.1186/s13059-023-02914-z	https://doi.org/10.1186/s13059-023-02914-z	Software methods publication	Only the major version is confirmed; minor versions are not inferred
Software or website algorithm	Python	Python	3.10.12 (retained methods record)	Database import, website backend and site-developed algorithms	Used by the website or supplied as a component	https://www.python.org/	https://www.python.org/downloads/	https://www.python.org/downloads/			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Historical methods record; not a claim that all current environments use the same version
Software or website algorithm	Flask	Flask	Not recorded	Website backend	Used by the website or supplied as a component	https://flask.palletsprojects.com/	https://flask.palletsprojects.com/en/stable/installation/	https://flask.palletsprojects.com/en/stable/installation/			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Official documentation; no specific software publication
Software or website algorithm	Jinja2	Jinja2	Not recorded	Page-template rendering	Used by the website or supplied as a component	https://jinja.palletsprojects.com/	https://jinja.palletsprojects.com/en/stable/intro/	https://jinja.palletsprojects.com/en/stable/intro/			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Official documentation; no specific software publication
Software or website algorithm	SQLite	SQLite	Not recorded	Relational database storage	Used by the website or supplied as a component	https://sqlite.org/	https://sqlite.org/download.html	https://sqlite.org/download.html			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Database engine; no specific software publication
Software or website algorithm	NumPy	NumPy	Exact version not recorded	LocPro feature and array processing	Used by the website or supplied as a component	https://numpy.org/	https://github.com/numpy/numpy	https://github.com/numpy/numpy/releases		REF030	Array programming with NumPy	2020	10.1038/s41586-020-2649-2	https://doi.org/10.1038/s41586-020-2649-2	Software methods publication	Computational dependency; not a separate localization method
Software or website algorithm	pandas	pandas	2.0.3 in the LocPro environment (retained methods record)	LocPro feature-table and result-table processing	Used by the website or supplied as a component	https://pandas.pydata.org/	https://github.com/pandas-dev/pandas	https://github.com/pandas-dev/pandas/releases		REF031	Data Structures for Statistical Computing in Python	2010	10.25080/Majora-92bf1922-00a	https://doi.org/10.25080/Majora-92bf1922-00a	Software methods publication	Data-processing dependency
Software or website algorithm	PyTorch	PyTorch	2.4.1+cpu in the LocPro environment (retained methods record)	LocPro/ESM2 inference	Used by the website or supplied as a component	https://pytorch.org/	https://github.com/pytorch/pytorch	https://pytorch.org/get-started/locally/		REF032	PyTorch: An Imperative Style, High-Performance Deep Learning Library	2019		https://proceedings.neurips.cc/paper/2019/hash/bdbca288fee7f92f2bfa9f7012727740-Abstract.html	Official technical documentation; no specific methods paper	No DOI confirmed for the framework paper; official NeurIPS publication URL retained
Software or website algorithm	Gunicorn	Gunicorn	Current system service; exact version not recorded	Python web-service worker processes	Used by the website or supplied as a component	https://gunicorn.org/	https://github.com/benoitc/gunicorn	https://github.com/benoitc/gunicorn			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Does not provide independent biological evidence for algorithmic results
Software or website algorithm	nginx	nginx	Software confirmed by the public HTTP response; exact build not recorded	Public reverse proxy and static-resource serving	Used by the website or supplied as a component	https://nginx.org/	https://nginx.org/en/download.html	https://nginx.org/en/download.html			No explicitly associated publication identified				Official technical documentation; no specific methods paper	Website infrastructure; official documentation, with no specific software publication
Software or website algorithm	SITE_QPCR	Website qPCR primer design	Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a	rubber_qpcr.py: sequence enumeration, melting-temperature and GC filtering, and transcript/genome specificity checks	Site-developed algorithm	http://47.95.224.165/rubber/tools	Site-developed; no independent public source-code repository released	No standalone download package released			No explicitly associated publication identified				No independent software publication	Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed
Software or website algorithm	SITE_CRISPR	Website CRISPR guide design	Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a	rubber_crispr.py: candidate SpCas9 NGG sites and reference-sequence off-target scanning	Site-developed algorithm	http://47.95.224.165/rubber/tools	Site-developed; no independent public source-code repository released	No standalone download package released			No explicitly associated publication identified				No independent software publication	Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed
Software or website algorithm	SITE_TFBS_SCAN	Website on-demand TFBS scanning	Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a	rubber_app.py: motif probability-matrix scanning of 4000-bp upstream regions or user-submitted sequences	Site-developed algorithm	http://47.95.224.165/rubber/tools	Site-developed; no independent public source-code repository released	No standalone download package released			No explicitly associated publication identified				No independent software publication	Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed
Software or website algorithm	SITE_SEQUENCE_TOOLS	Website sequence and homologous-arm tools	Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a	rubber_sequence.py and website tools: translation, sequence processing and homologous-arm assistance	Site-developed algorithm	http://47.95.224.165/rubber/tools	Site-developed; no independent public source-code repository released	No standalone download package released			No explicitly associated publication identified				No independent software publication	Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed
Reference database	UniProtKB / Swiss-Prot	UniProtKB / Swiss-Prot	Reviewed Swiss-Prot; exact historical download release not recorded	Homology-based transfer of functional annotations, GO terms and KEGG gene cross-references		https://www.uniprot.org/		https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz		REF033	UniProt: the Universal Protein Knowledgebase in 2025	2025	10.1093/nar/gkae1010	https://doi.org/10.1093/nar/gkae1010	Database resource publication	Homology-based transfer; original GO evidence codes retained, without implying experiments on the target gene
Reference database	Pfam (2021 publication)	Pfam (2021 publication)	Pfam-A; exact historical database release not recorded	HMMER domains and candidate transcription-factor families		https://www.ebi.ac.uk/interpro/entry/pfam/		https://www.ebi.ac.uk/interpro/download/Pfam/		REF034	Pfam: The protein families database in 2021	2021	10.1093/nar/gkaa913	https://doi.org/10.1093/nar/gkaa913	Database resource publication	Actual Pfam input cited; no InterProScan execution claimed
Reference database	STRING v12.0	STRING v12.0	12.0 (actual source manifest)	Homology-based transfer of Arabidopsis associations		https://version-12-0.string-db.org/		https://stringdb-static.org/download/protein.links.v12.0/3702.protein.links.v12.0.txt.gz		REF035	The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest	2023	10.1093/nar/gkac1000	https://doi.org/10.1093/nar/gkac1000	Database resource publication	Cross-species functional associations; not physical interactions demonstrated in Taraxacum kok-saghyz
Reference database	JASPAR 2024 (conditional on actual release)	JASPAR 2024 (conditional on actual release)	JASPAR2024 CORE plants non-redundant (retained source record)	Plant motifs and candidate transcription-factor binding sites		https://jaspar.elixir.no/		https://jaspar.genereg.net/downloads/		REF036	JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles	2024	10.1093/nar/gkad1059	https://doi.org/10.1093/nar/gkad1059	Database resource publication	Candidate sites; no direct binding demonstrated
Reference database	PlantTFDB	PlantTFDB	5.0 (download endpoint in retained motif-transfer scripts)	Experimental donor motifs transferred to TK1151 through homology/reciprocal best hits		https://planttfdb.gao-lab.org/		https://planttfdb.gao-lab.org/download/motif/PlantTFDB_TF_binding_motifs_from_experiments.gz		REF037	PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants	2017	10.1093/nar/gkw982	https://doi.org/10.1093/nar/gkw982	Database resource publication	Experimental motifs from donor species are not experimental evidence for the target transcription factor
Reference database	3did	3did	3did_flat.gz; historical release date not recorded	Pfam-domain contact compatibility support		https://3did.irbbarcelona.org/		https://3did.irbbarcelona.org/		REF038	3did: a catalog of domain-based interactions of known three-dimensional structure	2014	10.1093/nar/gkt887	https://doi.org/10.1093/nar/gkt887	Database resource publication	Domain-contact support; no website AlphaFold or molecular-docking result claimed
Reference database	Gene Ontology (original)	Gene Ontology (original)	GO identifiers, namespaces and taxon constraints retained; historical ontology revision not recorded	GO terms and taxonomic-incompatibility screening		https://geneontology.org/docs/go-citation-policy/		https://geneontology.org/docs/download-ontology/		REF039	Gene Ontology: tool for the unification of biology	2000	10.1038/75556	https://doi.org/10.1038/75556	Database resource publication	Annotation summaries provided; enrichment significance testing is not provided
Reference database	KEGG	KEGG	Swiss-Prot DAT KEGG gene cross-references; no native KO annotation generated	KEGG gene cross-references and candidate-pathway support		https://www.kegg.jp/		https://www.kegg.jp/kegg/rest/keggapi.html		REF040	KEGG: biological systems database as a model of the real world	2025	10.1093/nar/gkae909	https://doi.org/10.1093/nar/gkae909	Database resource publication	Gene cross-references are not complete KO annotations or pathway enrichment; the actual upstream source is UniProt DAT