{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T03:18:25Z","timestamp":1775791105534,"version":"3.50.1"},"reference-count":72,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2018,9,6]],"date-time":"2018-09-06T00:00:00Z","timestamp":1536192000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PD\/BD\/113969\/2015"],"award-info":[{"award-number":["PD\/BD\/113969\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BPD\/111148\/2015"],"award-info":[{"award-number":["SFRH\/BPD\/111148\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BPD\/77900\/2011"],"award-info":[{"award-number":["SFRH\/BPD\/77900\/2011"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BPD\/100912\/2014"],"award-info":[{"award-number":["SFRH\/BPD\/100912\/2014"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["IF\/01356\/2012"],"award-info":[{"award-number":["IF\/01356\/2012"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UID\/BIM\/04501\/2013"],"award-info":[{"award-number":["UID\/BIM\/04501\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UID\/CEC\/00127\/2013"],"award-info":[{"award-number":["UID\/CEC\/00127\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UID\/AMB\/50017"],"award-info":[{"award-number":["UID\/AMB\/50017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTCD\/EEI-SII\/6608\/2014"],"award-info":[{"award-number":["PTCD\/EEI-SII\/6608\/2014"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.<\/jats:p>","DOI":"10.3390\/genes9090445","type":"journal-article","created":{"date-parts":[[2018,9,6]],"date-time":"2018-09-06T10:38:38Z","timestamp":1536230318000},"page":"445","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-552X","authenticated-orcid":false,"given":"Diogo","family":"Pratas","sequence":"first","affiliation":[{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8962-8985","authenticated-orcid":false,"given":"Morteza","family":"Hosseini","sequence":"additional","affiliation":[{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"given":"Gon\u00e7alo","family":"Grilo","sequence":"additional","affiliation":[{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9164-0016","authenticated-orcid":false,"given":"Armando J.","family":"Pinho","sequence":"additional","affiliation":[{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5926-8042","authenticated-orcid":false,"given":"Raquel M.","family":"Silva","sequence":"additional","affiliation":[{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Institute for Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9157-8761","authenticated-orcid":false,"given":"T\u00e2nia","family":"Caetano","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-2395","authenticated-orcid":false,"given":"Jo\u00e3o","family":"Carneiro","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8950-1036","authenticated-orcid":false,"given":"Filipe","family":"Pereira","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2018,9,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1146\/annurev.genet.37.110801.143214","article-title":"Genetic analyses from ancient DNA","volume":"38","author":"Poinar","year":"2004","journal-title":"Annu. Rev. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1126\/science.1084114","article-title":"Diverse plant and animal genetic records from Holocene and Pleistocene sediments","volume":"300","author":"Willerslev","year":"2003","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.tree.2003.11.010","article-title":"Isolation of nucleic acids and cultures from fossil ice and permafrost","volume":"19","author":"Willerslev","year":"2004","journal-title":"Trends Ecol. Evolut."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1002\/bies.201400160","article-title":"The future of ancient DNA: Technical advances and conceptual shifts","volume":"37","author":"Hofreiter","year":"2015","journal-title":"BioEssays"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1111\/j.1751-8369.2008.00087.x","article-title":"Late Pleistocene fossil find in Svalbard: The oldest remains of a polar bear (Ursus maritimus Phipps, 1744) ever discovered","volume":"28","author":"Wiig","year":"2009","journal-title":"Polar Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5053","DOI":"10.1073\/pnas.0914266107","article-title":"Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear","volume":"107","author":"Lindqvist","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"E2382","DOI":"10.1073\/pnas.1210506109","article-title":"Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change","volume":"109","author":"Miller","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"46487","DOI":"10.1038\/srep46487","article-title":"The evolutionary history of bears is characterized by gene flow across species","volume":"7","author":"Kumar","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"6089","DOI":"10.3390\/v7112927","article-title":"An evolutionarily young polar bear (Ursus maritimus) endogenous retrovirus identified from next generation sequence data","volume":"7","author":"Tsangaras","year":"2015","journal-title":"Viruses"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nrmicro.2016.182","article-title":"Clinical and biological insights from viral genome sequencing","volume":"15","author":"Houldcroft","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3407","DOI":"10.1016\/j.cub.2016.10.061","article-title":"17th century variola virus reveals the recent history of smallpox","volume":"26","author":"Duggan","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nature21674","article-title":"Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus","volume":"544","author":"Weyrich","year":"2017","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13323-014-0017-4","article-title":"Editors\u2019 Pick: Contamination has always been the issue!","volume":"5","author":"Sajantila","year":"2014","journal-title":"Investig. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1111\/1755-0998.12546","article-title":"metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data","volume":"16","author":"Louvel","year":"2016","journal-title":"Mol. Ecol. Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: Ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Herbig, A., Maixner, F., Bos, K.I., Zink, A., Krause, J., and Huson, D.H. (2017). MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman. bioRxiv.","DOI":"10.1101\/050559"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"461","DOI":"10.14778\/2735479.2735480","article-title":"MRCSI: Compressing and searching string collections with multiple references","volume":"8","author":"Wandelt","year":"2015","journal-title":"Proc. VLDB Endow."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s40168-018-0460-1","article-title":"Flexible metagenome analysis using the MGX framework","volume":"6","author":"Jaenicke","year":"2018","journal-title":"Microbiome"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/bts665","article-title":"VirusSeq: Software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1101\/gr.171934.113","article-title":"A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples","volume":"24","author":"Naccache","year":"2014","journal-title":"Genome Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"23774","DOI":"10.1038\/srep23774","article-title":"VIP: An integrated pipeline for metagenomics of virus identification and discovery","volume":"6","author":"Li","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"40712","DOI":"10.1038\/srep40712","article-title":"Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer","volume":"7","author":"Zhang","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Rampelli, S., Soverini, M., Turroni, S., Quercia, S., Biagi, E., Brigidi, P., and Candela, M. (2016). ViromeScan: A new tool for metagenomic viral community profiling. BMC Genom., 17.","DOI":"10.1186\/s12864-016-2446-3"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s40168-017-0283-5","article-title":"VirFinder: A novel k-mer based tool for identifying viral sequences from assembled metagenomic data","volume":"5","author":"Ren","year":"2017","journal-title":"Microbiome"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Costea, P.I., Munch, R., Coelho, L.P., Paoli, L., Sunagawa, S., and Bork, P. (2017). metaSNV: A tool for metagenomic strain level analysis. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0182392"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1093\/bioinformatics\/btw290","article-title":"COCACOLA: Binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge","volume":"33","author":"Lu","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/bioinformatics\/btv584","article-title":"SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data","volume":"32","author":"Silva","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"329","DOI":"10.3389\/fgene.2015.00329","article-title":"riboFrame: An improved method for microbial taxonomy profiling from non-targeted metagenomics","volume":"6","author":"Ramazzotti","year":"2015","journal-title":"Front. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Kim, M., Zhang, X., Ligo, J., Farnoud, F., Veeravalli, V., and Milenkovic, O. (2016). MetaCRAM: An integrated pipeline for metagenomic taxonomy identification and compression. BMC Bioinform., 17.","DOI":"10.1186\/s12859-016-0932-x"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1186\/s13059-017-1319-7","article-title":"Alignment-free sequence comparison: Benefits, applications, and tools","volume":"18","author":"Zielezinski","year":"2017","journal-title":"Genome Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev-biodatasci-080917-013431","article-title":"Alignment-Free Sequence Analysis and Applications","volume":"1","author":"Ren","year":"2018","journal-title":"Annu. Rev. Biomed. Data Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e1034","DOI":"10.1002\/aps3.1034","article-title":"Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities","volume":"6","author":"Harbert","year":"2018","journal-title":"Appl. Plant Sci."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Pratas, D., Pinho, A.J., Silva, R.M., Rodrigues, J.M.O.S., Hosseini, M., Caetano, T., and Ferreira, P.J.S.G. (2018). FALCON-meta: A method to infer metagenomic composition of ancient DNA. bioRxiv.","DOI":"10.1101\/267179"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"15758","DOI":"10.1073\/pnas.1314445110","article-title":"Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments","volume":"110","author":"Dabney","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Pratas, D., Silva, R.M., and Pinho, A.J. (2018). Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes. Entropy, 20.","DOI":"10.3390\/e20060393"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Pinho, A.J., Pratas, D., and Ferreira, P.J.S.G. (April, January 30). Authorship attribution using relative compression. Proceedings of the 2016 Data Compression Conference, Snowbird, UT, USA.","DOI":"10.1109\/DCC.2016.53"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/2041-2223-5-9","article-title":"Validation of high throughput sequencing and microbial forensics applications","volume":"5","author":"Budowle","year":"2014","journal-title":"Investig. Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1073\/pnas.1318934111","article-title":"Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal","volume":"111","author":"Skoglund","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_45","first-page":"1682","article-title":"mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"23","author":"Ginolhac","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Schubert, M., Lindgreen, S., and Orlando, L. (2016). AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes, 9.","DOI":"10.1186\/s13104-016-1900-2"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Schubert, M., Ginolhac, A., Lindgreen, S., Thompson, J.F., Al-Rasheid, K.A., Willerslev, E., Krogh, A., and Orlando, L. (2012). Improving ancient DNA read mapping against modern reference genomes. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-178"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Taron, U.H., Lell, M., Barlow, A., and Paijmans, J.L. (2018). Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool. Genes, 9.","DOI":"10.3390\/genes9030157"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: Sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Dale","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Pratas, D., Pinho, A.J., and Ferreira, P.J.S.G. (April, January 30). Efficient compression of genomic sequences. Proceedings of the 2016 Data Compression Conference (DCC), Snowbird, UT, USA.","DOI":"10.1109\/DCC.2016.60"},{"key":"ref_52","unstructured":"Bell, T.C., Cleary, J.G., and Witten, I.H. (1990). Text Compression, Prentice Hall."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Pinho, A.J., Pratas, D., and Ferreira, P.J.S.G. (2011, January 28\u201330). Bacteria DNA sequence compression using a mixture of finite-context models. Proceedings of the 2011 IEEE Statistical Signal Processing Workshop (SSP), Nice, France.","DOI":"10.1109\/SSP.2011.5967637"},{"key":"ref_54","unstructured":"Pratas, D., and Pinho, A.J. (2014, January 1\u20135). Exploring deep Markov models in genomic data compression using sequence pre-analysis. Proceedings of the 2014 22nd European Signal Processing Conference (EUSIPCO), Lisbon, Portugal."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Pratas, D., Hosseini, M., and Pinho, A.J. (2017, January 21\u201323). Substitutional Tolerant Markov Models for Relative Compression of DNA Sequences. Proceedings of the International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal.","DOI":"10.1007\/978-3-319-60816-7_32"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Ferreira, P.J.S.G., and Pinho, A.J. (2014, January 4\u20139). Compression-based normal similarity measures for DNA sequences. Proceedings of the 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP-2014), Florence, Italy.","DOI":"10.1109\/ICASSP.2014.6853630"},{"key":"ref_57","unstructured":"Pratas, D. (2016). Compression and Analysis of Genomic Data. [Ph.D. Thesis, University of Aveiro]."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1093\/sysbio\/syw027","article-title":"Phylogenomics for Systematic Biology","volume":"65","author":"Posada","year":"2016","journal-title":"Syst. Biol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Pinho, A.J., Garcia, S.P., Pratas, D., and Ferreira, P.J. (2013). DNA sequences at a glance. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0079922"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Hosseini, M., Pratas, D., and Pinho, A.J. (2017, January 21\u201323). On the role of inverted repeats in DNA sequence similarity. Proceedings of the International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal.","DOI":"10.1007\/978-3-319-60816-7_28"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"4422","DOI":"10.1099\/ijsem.0.001367","article-title":"The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov","volume":"66","author":"Scholz","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1089\/cmb.2013.0084","article-title":"Assembling single-cell genomes and mini-metagenomes from chimeric MDA products","volume":"20","author":"Nurk","year":"2013","journal-title":"J. Comput. Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning DNA sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"E976","DOI":"10.1073\/pnas.1317064111","article-title":"Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis","volume":"111","author":"Naccache","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Strong, M.J., Xu, G., Morici, L., Bon-Durant, S.S., Baddoo, M., Lin, Z., Fewell, C., Taylor, C.M., and Flemington, E.K. (2014). Microbial contamination in next generation sequencing: Implications for sequence-based analysis of clinical samples. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004437"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"4070","DOI":"10.1128\/AEM.00428-08","article-title":"Isolation and characterization of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum","volume":"74","author":"Stenholm","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2494","DOI":"10.1038\/emboj.2009.222","article-title":"The Neandertal genome and ancient DNA authenticity","volume":"28","author":"Green","year":"2009","journal-title":"EMBO J."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"a012567","DOI":"10.1101\/cshperspect.a012567","article-title":"Ancient DNA damage","volume":"5","author":"Dabney","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.tig.2017.05.005","article-title":"Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication","volume":"33","author":"Key","year":"2017","journal-title":"Trends Genet."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2243","DOI":"10.1093\/bioinformatics\/btw139","article-title":"On genomic repeats and reproducibility","volume":"32","author":"Firtina","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/ng.437","article-title":"Personalized copy number and segmental duplication maps using next-generation sequencing","volume":"41","author":"Alkan","year":"2009","journal-title":"Nat. Genet."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/9\/445\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:19:11Z","timestamp":1760195951000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/9\/445"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,9,6]]},"references-count":72,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2018,9]]}},"alternative-id":["genes9090445"],"URL":"https:\/\/doi.org\/10.3390\/genes9090445","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,9,6]]}}}