PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38114921", "kind": "science-record", "revision": 3, "content_hash": "sha256:77048774656906b5e3bb24a3a126e61365188721d09ec157d3c0d8277f8f75ef", "created_at": "2026-11-01T19:20:03Z", "updated_at": "2026-11-01T22:10:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.", "doi": "10.1186/s12859-023-05613-5", "pmid": "38114921", "authors": ["Kateřina Faltejsková", "Jiří Vondrášek"], "journal": "BMC bioinformatics", "year": 2023, "abstract": "BACKGROUND: The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome.\nRESULTS: We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods.\nCONCLUSIONS: We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo ( https://doi.org/10.5281/zenodo.7116424 ).", "claims": [{"id": "claim-method", "statement": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[8] \"Peak calling\" paragraph 5", "quote": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PAPerFly yields better results than an aggregation of ChIP-seq agnostic tools.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38114921", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PAPerFly yields better results than an aggregation of ChIP-seq agnostic tools.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38114921"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE11431"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE11431"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38114921", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12859-023-05613-5", "sha256": "sha256:3cd3631a542dd4597c6e1b9f44241c121672ebd9bfd364d6258ad8bf2fac9404", "bytes": 37758, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12859-023-05613-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10731698", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11431", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11431", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11431", "version": null, "note": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM288345", "GSM288346", "GSM288347", "GSM288348", "GSM288349", "GSM288350", "GSM288351", "GSM288352", "GSM288353", "GSM288354", "GSM288355", "GSM288356", "GSM288357", "GSM288358", "GSM288359", "GSM288360"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "9185", "taxon": "Mus musculus", "title": "Mapping of transcription factor binding sites in mouse embryonic stem cells", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE11431 not downloaded", "asset:data:geo:GSE11431 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "Blast"}}, {"id": "method-2", "family": null, "specific": null, "label": "Mann–Whitney U test with Bonferroni correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, we compare the segment in the array of abundances corresponding to a treatment replicate with the segment in the respective control abundances array segment using a Mann–Whitney U test [29] with Bonferroni correction [30]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE11431"], "resolved_accessions": ["GSE11431"], "statements": ["The mouse dataset is available in the SRA under the identifier GSE11431. The human datasets analysed during the current study are available in the ENCODE database under the following identifiers: ENCSR490LWA, ENCSR065XVO, ENCSR093FKD, ENCFF000VPU (controlled by ENCFF002ECM), ENCFF002EDN (controlled by ENCFF000PPC), ENCFF000QLL (controlled by ENCFF001HUM), ENCFF000WDW (controlled by ENCFF002ECR), ENCFF000XML (controlled by ENCFF000XOO), ENCFF000YOW (controlled by ENCFF000YOV), ENCFF000ZBR (controlled by ENCFF000YOV), ENCFF263VVK (controlled by ENCFF304HKO), ENCFF489ABL (controlled by ENCFF002DTU), ENCFF156EZY (controlled by ENCFF168MST), ENCFF424HPQ (controlled by ENCFF002DTU), ENCFF903KXG (controlled by ENCFF513OBT), ENCFF002ELA (controlled by ENCFF002EFT), ENCFF793WFY (controlled by ENCFF002EFF).The code is available on Github (https://github.com/Caeph/paperfly) or on Zenodo (https://doi.org/10.5281/zenodo.711642). A docker image is also available on dockerhub (caeph/paperfly).Operating system(s): Unix-based. Programming language: Python, C#, bash. Other requirements: Python 3.8 or higher, jellyfish 2.3.0 (https://github.com/gmarcais/Jellyfish), BCALM 2 version 1.4.1 ( https://github.com/GATB/bcalm). For C# program compilation: Mono JIT compiler version 6.12.0 and NuGet version 6.2.1. License: MS-PL for the C# part of the program, BSD-3-Clause otherwise. Any restrictions to use by non-academics: none."], "basis": "The paper names GSE11431 in SRA and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:38114921", "data:geo:GSE11431"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11431"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:03:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10942, "completion_tokens": 2741, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38114921", "type": "paper", "label": "pmid:38114921"}, {"id": "source:pmid:38114921", "type": "manuscript", "label": "PMID 38114921 full text"}, {"id": "data:geo:GSE11431", "type": "dataset", "label": "GEO GSE11431"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38114921", "type": "paper", "label": "pmid:38114921"}, {"id": "source:pmid:38114921", "type": "manuscript", "label": "PMID 38114921 full text"}, {"id": "data:geo:GSE11431", "type": "dataset", "label": "GEO GSE11431"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38114921", "type": "extraction", "used": ["source:pmid:38114921"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11431", "type": "accession_resolution", "used": ["data:geo:GSE11431"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38114921", "parent_hash": "sha256:7b458b31e715aaeb9e5c3498512ae1c6c1c1f07afe2cf09b086d9b67bf3b00bc", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE11431 licence not read", "asset:data:geo:GSE11431 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ur approach was tested by processing several ChIP-seq experiments available in the ENCODE database", "yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available", "APerFly takes in raw sequencing reads from a ChIP-seq experiment (or similar; our workflow does no", "assumptions about the particularities of the ChIP-seq experiment design) and the size of k-mer (th"], "order_basis": "paper_text_order:1141", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["espective significance. Method comparison on mouse embryonic stem cells (ESC) To compare our to", "ed their analysis on a ChIP-seq dataset from mouse embryonic stem cells (GSE11431) [31]. First,", "we mapped the results of our analysis to the mouse reference genome (mm8, to be consistent with", "ed with mapping the PAPerFly chiptigs to the mouse genome. Then, we checked whether the PAPerFl"], "order_basis": "paper_text_order:1911", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Blast"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}