{"id":"https://openalex.org/W2951893579","doi":"https://doi.org/10.1093/bioinformatics/btz144","title":"Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences","display_name":"Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences","publication_year":2019,"publication_date":"2019-02-22","ids":{"openalex":"https://openalex.org/W2951893579","doi":"https://doi.org/10.1093/bioinformatics/btz144","mag":"2951893579","pmid":"https://pubmed.ncbi.nlm.nih.gov/30799504"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/19/3826/30061651/btz144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/19/3826/30061651/btz144.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088370475","display_name":"Kirill Kryukov","orcid":"https://orcid.org/0000-0002-0286-0288"},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kirill Kryukov","raw_affiliation_strings":["Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan","institution_ids":["https://openalex.org/I1314466530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064404027","display_name":"Mahoko Takahashi Ueda","orcid":"https://orcid.org/0000-0002-3960-0922"},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mahoko Takahashi Ueda","raw_affiliation_strings":["Micro/Nano Technology Center, Tokai University , Hiratsuka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Micro/Nano Technology Center, Tokai University , Hiratsuka, Japan","institution_ids":["https://openalex.org/I1314466530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054739143","display_name":"So Nakagawa","orcid":"https://orcid.org/0000-0003-1760-3839"},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"So Nakagawa","raw_affiliation_strings":["Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan","Micro/Nano Technology Center, Tokai University , Hiratsuka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan","institution_ids":["https://openalex.org/I1314466530"]},{"raw_affiliation_string":"Micro/Nano Technology Center, Tokai University , Hiratsuka, Japan","institution_ids":["https://openalex.org/I1314466530"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023402430","display_name":"Tadashi Imanishi","orcid":"https://orcid.org/0000-0002-1182-9127"},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tadashi Imanishi","raw_affiliation_strings":["Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Japan","institution_ids":["https://openalex.org/I1314466530"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088370475"],"corresponding_institution_ids":["https://openalex.org/I1314466530"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.2075,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.95295272,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"19","first_page":"3826","last_page":"3828"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.6629999876022339,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.6629999876022339,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.1354999989271164,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.06939999759197235,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lossless-compression","display_name":"Lossless compression","score":0.8098239898681641},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7832043170928955},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.49487847089767456},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4669801890850067},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4386724829673767},{"id":"https://openalex.org/keywords/huffman-coding","display_name":"Huffman coding","score":0.4369544982910156},{"id":"https://openalex.org/keywords/compression","display_name":"Compression (physics)","score":0.4143468141555786},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3860200047492981},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.35229426622390747},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.29330307245254517},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.25555551052093506},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22137519717216492}],"concepts":[{"id":"https://openalex.org/C81081738","wikidata":"https://www.wikidata.org/wiki/Q55542","display_name":"Lossless compression","level":3,"score":0.8098239898681641},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7832043170928955},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.49487847089767456},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4669801890850067},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4386724829673767},{"id":"https://openalex.org/C46900642","wikidata":"https://www.wikidata.org/wiki/Q2647","display_name":"Huffman coding","level":3,"score":0.4369544982910156},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.4143468141555786},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3860200047492981},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.35229426622390747},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.29330307245254517},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.25555551052093506},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22137519717216492},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/19/3826/30061651/btz144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30799504","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30799504","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5733259","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6761962","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/19/3826/30061651/btz144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1931027898","https://openalex.org/W2028990382","https://openalex.org/W2157745386","https://openalex.org/W2158678815","https://openalex.org/W2561200699","https://openalex.org/W4231108571"],"related_works":["https://openalex.org/W1557642114","https://openalex.org/W1762028264","https://openalex.org/W2948148442","https://openalex.org/W2461250372","https://openalex.org/W2394342941","https://openalex.org/W2169853506","https://openalex.org/W2547124190","https://openalex.org/W2350586049","https://openalex.org/W2385628723","https://openalex.org/W2169871401"],"abstract_inverted_index":{"SUMMARY:":[0],"DNA":[1,48,60],"sequence":[2],"databases":[3],"use":[4],"compression":[5,31,41],"such":[6],"as":[7,83,85],"gzip":[8],"to":[9,45],"reduce":[10],"the":[11,46,105],"required":[12],"storage":[13],"space":[14],"and":[15,34,63,65,74,81,99],"network":[16],"transmission":[17],"time.":[18],"We":[19,55],"describe":[20],"Nucleotide":[21,38],"Archival":[22,39],"Format":[23,40,92],"(NAF)-a":[24],"new":[25],"file":[26],"format":[27,58,86],"for":[28,109],"lossless":[29],"reference-free":[30],"of":[32],"FASTA":[33],"FASTQ-formatted":[35],"nucleotide":[36],"sequences.":[37],"ratio":[42],"is":[43,94],"comparable":[44],"best":[47],"compressors,":[49],"while":[50],"providing":[51],"dramatically":[52],"faster":[53],"decompression.":[54],"compared":[56],"our":[57],"with":[59,66],"compressors:":[61,69],"DELIMINATE":[62],"MFCompress,":[64],"general":[67],"purpose":[68],"gzip,":[70],"bzip2,":[71],"xz,":[72],"brotli":[73],"zstd.":[75],"AVAILABILITY":[76],"AND":[77],"IMPLEMENTATION:":[78],"NAF":[79],"compressor":[80],"decompressor,":[82],"well":[84],"specification":[87,93],"are":[88,101,117],"available":[89,118],"at":[90,119],"https://github.com/KirillKryukov/naf.":[91],"in":[95],"public":[96],"domain.":[97],"Compressor":[98],"decompressor":[100],"open":[102],"source":[103],"under":[104],"zlib/libpng":[106],"license,":[107],"free":[108],"nearly":[110],"any":[111],"use.":[112],"SUPPLEMENTARY":[113],"INFORMATION:":[114],"Supplementary":[115],"data":[116],"Bioinformatics":[120],"online.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
