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Journal articles on the topic 'Barcode library'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Blois, Sylvain, Benjamin M. Goetz, James J. Bull, and Christopher S. Sullivan. "Interpreting and de-noising genetically engineered barcodes in a DNA virus." PLOS Computational Biology 18, no. 11 (2022): e1010131. http://dx.doi.org/10.1371/journal.pcbi.1010131.

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The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe th

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Fahldieck, Moritz, Björn Rulik, Jana Thormann, and Ximo Mengual. "A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany." Biodiversity Data Journal 12 (September 24, 2024): e127190. https://doi.org/10.3897/BDJ.12.e127190.

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Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination.In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. O

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Stuart, Julius D., Natalie R. Wickenkamp, Kaleb A. Davis, Camden Meyer, Rebekah C. Kading, and Christopher D. Snow. "Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications." International Journal of Molecular Sciences 24, no. 3 (2023): 2549. http://dx.doi.org/10.3390/ijms24032549.

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Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allo

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Sikes, Derek S., Matthew Bowser, John M. Morton, Casey Bickford, Sarah Meierotto, and Kyndall Hildebrandt. "Building a DNA barcode library of Alaska’s non-marine arthropods." Genome 60, no. 3 (2017): 248–59. http://dx.doi.org/10.1139/gen-2015-0203.

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Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of whi

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Mandal, Sukumar. "Designing Barcode Generation Interface: A Methodology of an Integrated Framework for Libraries." Asian Journal of Information Science and Technology 7, no. 2 (2017): 16–20. http://dx.doi.org/10.51983/ajist-2017.7.2.156.

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Nowadays libraries are facing the challenges posed by a diverse and rapidly expanding information universe. Increased user expectations for faster and easier access to relevant information go hand in hand with institutional demands for increased operational efficiency. Integrated library system required to makes it easier for housekeeping operations in a library. Barcode is a part of housekeeping operation. The process of library automation in different aspects also helps to make better use of existing library services and staff. It allows for the improvement of library in the variety, amount

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Huemer, Peter, Ole Karsholt, Leif Aarvik, et al. "DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity." ZooKeys 921 (March 24, 2020): 141–57. http://dx.doi.org/10.3897/zookeys.921.49199.

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For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but

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Huemer, Peter, Ole Karsholt, Leif Aarvik, et al. "DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity." ZooKeys 921 (March 24, 2020): 141–57. https://doi.org/10.3897/zookeys.921.49199.

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For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but

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Gunawan, Arief. "PEMANFAATAN APLIKASI SLIMS SENAYAN VERSI 7 CENDANA PORTABLE DALAM PEMBUATAN BARCODE KOLEKSI PERPUSTAKAAN PUSAT RISET PERIKANAN." Jurnal Pari 3, no. 2 (2018): 113. http://dx.doi.org/10.15578/jp.v3i2.6804.

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ABSTRAKPembuatan kode batang (barcode) merupakan salah satu kegiatan perpustakaan dalam penerapan pencariankembali buku dan pengembalian ke tempat rak buku dengan lebih mudah dengan menggunakan teknologi informasi.Slims Senayan merupakan salah satu program perpustakaan yang dalam pilihan menunya ada pembuatan barcode yangbisa digunakan pustakawan dengan cara yang mudah digunakan sehingga bisa lebih bermanfaat dalam pengelolaankoleksi perpustakaan dan memanfaatkan teknologi informasi. Dalam proses pengecekan barcode digunakan hardware“barcode scanner”. Dengan penggunaan barcode ini diharapkan p

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Mabragaña, Ezequiel, Valeria Gabbanelli, Florencia Matusevich, et al. "DNA Barcoding Southwestern Atlantic Skates: A 20-Year Effort in Building a Species Identification Library." Diversity 17, no. 5 (2025): 311. https://doi.org/10.3390/d17050311.

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The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specime

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Jażdżewska, Anna Maria, Anne Helene S. Tandberg, Tammy Horton, and Saskia Brix. "Global gap-analysis of amphipod barcode library." PeerJ 9 (November 4, 2021): e12352. http://dx.doi.org/10.7717/peerj.12352.

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In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a

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Specchia, Valeria, Eftychia Tzafesta, Gabriele Marini, Salvatore Scarcella, Simona D’Attis, and Maurizio Pinna. "Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy)." Journal of Marine Science and Engineering 8, no. 7 (2020): 538. http://dx.doi.org/10.3390/jmse8070538.

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The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our a

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Raupach, Michael J., Björn Rulik, and Jörg Spelda. "Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)." ZooKeys 1082 (January 20, 2022): 103–25. http://dx.doi.org/10.3897/zookeys.1082.69851.

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DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Br

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Raupach, Michael J., Björn Rulik, and Jörg Spelda. "Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)." ZooKeys 1082 (January 20, 2022): 103–25. https://doi.org/10.3897/zookeys.1082.69851.

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DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Br

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Rahmadani, Dandi, and Rachmat Aulia. "Pemanfaatan Library Zxing Sebagai Pembaca Barcode pada Aplikasi Sistem Inventory Toko Pakaian." Jurnal Ilmu Komputer dan Sistem Komputer Terapan (JIKSTRA) 4, no. 1 (2022): 19–30. http://dx.doi.org/10.35447/jikstra.v4i1.535.

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Rapidly developing applications have provided enermous benefits for small and medium enterprises activities such as clothing stores. Therefore we need a good inventory system in a clothing store. In this study, the author will design an android-based inventory application system that will be implemented in a clothing store. This applications was built by utilizing a mobile device as a media processing clothing inventory system. This application will utilize the android device’s camera as a barcode scanner or barcode reader. So that, all sales transactions will be done through a barcode scanner

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Rimet, Frédéric, Eva Aylagas, Angel Borja, et al. "Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life." Metabarcoding and Metagenomics 5 (February 26, 2021): e58056. https://doi.org/10.3897/mbmg.5.58056.

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DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstre

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Hawkins, John A., Stephen K. Jones, Ilya J. Finkelstein, and William H. Press. "Indel-correcting DNA barcodes for high-throughput sequencing." Proceedings of the National Academy of Sciences 115, no. 27 (2018): E6217—E6226. http://dx.doi.org/10.1073/pnas.1802640115.

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Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we pr

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Marthinsen, Gunnhild, Siri Rui, and Einar Timdal. "OLICH: A reference library of DNA barcodes for Nordic lichens." Biodiversity Data Journal 7 (August 19, 2019): e36252. https://doi.org/10.3897/BDJ.7.e36252.

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DNA barcodes are increasingly being used for species identification amongst the lichenised fungi. This paper presents a dataset aiming to provide an authoritative DNA barcode sequence library for a wide array of Nordic lichens. We present 1324 DNA barcode sequences (nrITS) for 507 species in 175 genera and 25 orders. Thirty-eight species are new to GenBank and, for 25 additional species, ITS sequences are here presented for the first time. The dataset covers 20–21% of the Nordic lichenised species. Barcode gap analyses are given and discussed for the three genera <i>Cladonia</i>, <i>Ramalina</

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Raupach, Michael J., Karsten Hannig, Jérome Morinière, and Lars Hendrich. "A DNA barcode library for ground beetles of Germany: the genus Agonum Bonelli, 1810 (Insecta, Coleoptera, Carabidae)." Deutsche Entomologische Zeitschrift 67, no. 2 (2020): 197–207. http://dx.doi.org/10.3897/dez.67.56163.

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The ground beetle genus Agonum Bonelli, 1810 is a large genus of the tribe Platynini with many species that show high amounts of intraspecific variations, making a correct identification challenging. As part of the German Barcode of Life initiative, this publication provides a comprehensive DNA barcode library for species of Agonum that are reported for Germany. In total, DNA barcodes from 258 beetles and 23 species were analysed using the Barcode of Life Data System (BOLD) workbench, including sequences from former studies and 68 newly-generated sequences. The neighbour-joining analyses, base

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Raupach, Michael J., Karsten Hannig, Jérome Morinière, and Lars Hendrich. "A DNA barcode library for ground beetles of Germany: the genus Agonum Bonelli, 1810 (Insecta, Coleoptera, Carabidae)." Deutsche Entomologische Zeitschrift 67, no. (2) (2020): 197–207. https://doi.org/10.3897/dez.67.56163.

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The ground beetle genus Agonum Bonelli, 1810 is a large genus of the tribe Platynini with many species that show high amounts of intraspecific variations, making a correct identification challenging. As part of the German Barcode of Life initiative, this publication provides a comprehensive DNA barcode library for species of Agonum that are reported for Germany. In total, DNA barcodes from 258 beetles and 23 species were analysed using the Barcode of Life Data System (BOLD) workbench, including sequences from former studies and 68 newly-generated sequences. The neighbour-joining analyses, base

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Huemer, Peter, and Marko Mutanen. "An Incomplete European Barcode Library Has a Strong Impact on the Identification Success of Lepidoptera from Greece." Diversity 14, no. 2 (2022): 118. http://dx.doi.org/10.3390/d14020118.

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Species identification by means of DNA barcodes depends essentially on the scope and quality of a relevant reference library. The first analysis of a large number (about 600 morphospecies) of southern European Lepidoptera (Greece: Peloponnese) shows both the advantages and disadvantages with regard to a reliable identification of Mediterranean species. We determined 946 DNA barcode sequences from 47 families, of which 929 sequences from 46 families were successfully assigned to a Barcode Index Number (BIN) in the global Barcode of Life Data Systems (BOLD) database. A species level identificati

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Hajibabaei, Mehrdad, Jeremy R. deWaard, Natalia V. Ivanova, et al. "Critical factors for assembling a high volume of DNA barcodes." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (2005): 1959–67. http://dx.doi.org/10.1098/rstb.2005.1727.

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Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for pr

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Jung, Jungham, Bohyeon Yu, Owen Hoare, and Aaron Diaz. "METB-13. A SINGLE-CELL GENETIC IN VIVO LINEAGE-TRACING PLATFORM FOR MEDULLOBLASTOMA." Neuro-Oncology 25, Supplement_1 (2023): i33. http://dx.doi.org/10.1093/neuonc/noad073.130.

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Abstract Comparative single-cell studies of group 3/4 medulloblastomas (MBs) and fetal brain have identified a common hierarchy of glutamatergic-lineage cell types and an apparent cell-of-origin in the rhombic lip. An increased understanding of the genetic regulators of stem-cell maintenance and differentiation in MB would clearly be of therapeutic benefit. There is a significant need for lineage-tracing systems to model MB malignant transformation, progression, and response to therapy. We developed in vivo and in organoid genetic lineage-tracing systems with a single-cell readout. A high-comp

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Bikashvili, Ani, Nino Kachlishvili, Bella Japoshvili, and Levan Mumladze. "Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus." Biodiversity Data Journal 10 (September 13, 2022): e84887. https://doi.org/10.3897/BDJ.10.e84887.

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This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs dive

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Sonet, Gontran, Kurt Jordaens, Yves Braet, et al. "Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France." ZooKeys 365 (December 30, 2013): 307–28. https://doi.org/10.3897/zookeys.365.6027.

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Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available.We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome <i>c </i>oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two publ

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Vella, Adriana, Clare Marie Mifsud, Denis Magro, and Noel Vella. "DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity." Diversity 14, no. 12 (2022): 1090. http://dx.doi.org/10.3390/d14121090.

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This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and use

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Hsu, Christopher H., Shaina Porter, Gareth Highnam, David Mittelman, and Matthew H. Porteus. "Population Dynamics of Acute Myeloid Leukemia Clones by Barcode Tracking and High Throughput Sequencing." Blood 120, no. 21 (2012): 1398. http://dx.doi.org/10.1182/blood.v120.21.1398.1398.

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Abstract Abstract 1398 Introduction: Acute myeloid leukemia (AML) is a heterogeneous malignancy that continues to have a significant relapse rate in both adult and pediatric patients. This heterogeneity manifests itself between patients because different patients will have different gene mutations causing their AML (inter-patient heterogeneity). It also manifests as intra-patient heterogeneity as within a single patient there are different sub-clones that contribute differentially to primary disease and relapse. For example, relapse after chemotherapy can occur from a genetically distinct sub-

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D’Ercole, Jacopo, Vlad Dincă, Paul A. Opler, et al. "A DNA barcode library for the butterflies of North America." PeerJ 9 (April 19, 2021): e11157. http://dx.doi.org/10.7717/peerj.11157.

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Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were mo

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Huemer, Peter, Christian Wieser, Wolfgang Stark, Paul Hebert, and Benjamin Wiesmair. "DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) – a nearly perfect match of Linnean taxonomy." Biodiversity Data Journal 7 (August 7, 2019): e37734. https://doi.org/10.3897/BDJ.7.e37734.

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The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obt

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Laurito, M., A. M. Ayala, D. L. Arias-Builes, and W. R. Almirón. "Improving the DNA Barcode Library of Mosquito Species With New Identifications and Discoveries in North-Central Argentina." Journal of Medical Entomology 59, no. 1 (2021): 173–83. http://dx.doi.org/10.1093/jme/tjab160.

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Abstract The family Culicidae is represented by 244 species in Argentina, many of them with epidemiological importance. DNA barcodes are effective tools for identifying mosquito species, for knowing genetic variability, and for establishing phylogenetic relationships. This work aims to explore mosquito diversity employing different species delimitation approaches and to establish formally a DNA barcode library for the Argentinian mosquito fauna. Barcode fragments of 80 specimens of Argentinian mosquitoes of 28 species of the genera Aedeomyia Theobald (Diptera: Culicidae), Anopheles Meigen (Dip

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Mr., Amit Arvind Gurav. "QR Code And Library Services." International Journal of Advance and Applied Research 10, no. 1 (2022): 310 to 313. https://doi.org/10.5281/zenodo.7192293.

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<em>The full form of QR code is Quick Response code. The QR code technology is just like the barcode technology. The differences between barcode technology and QR code technology is that barcode technology can handle the information only in horizontal direction and QR code technology can handle the information in both horizontal and vertical direction. QR code technology is widely used as a medium to deliver a message to end users. The QR codes are mainly used by libraries for the purpose of promoting their services. Nowadays the QR code technology is widely used by many libraries for providin

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Pešić, Vladimir, Andrzej Zawal, Sónia Ferreira, et al. "DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia)." ZooKeys 1217 (October 31, 2024): 119–71. http://dx.doi.org/10.3897/zookeys.1217.131730.

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This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticola soniae Pešić, sp. nov. and T. elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now hav

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Pešić, Vladimir, Andrzej Zawal, Sónia Ferreira, et al. "DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia)." ZooKeys 1217 (October 31, 2024): 119–71. https://doi.org/10.3897/zookeys.1217.131730.

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This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, <i>Torrenticola soniae</i> Pešić, sp. nov. and <i>T. elisabethae</i> Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Po

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Melo, Martim, Rita Covas, Ricardo Lima, et al. "DNA Barcode library of the endemic-rich avifauna of the oceanic islands of the Gulf of Guinea." Biodiversity Data Journal 11 (October 23, 2023): e110428. https://doi.org/10.3897/BDJ.11.e110428.

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The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morphologically identified to species or subspecies level by qualified ornithologists. The dataset includes all endemic species and 3/4 of the extant endemic subspecies of the islands. This dataset is the second release by BioSTP and it greatly increases

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Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. http://dx.doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa.

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Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. https://doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa.

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Valdez-Moreno, Martha, Manuel Mendoza-Carranza, Eduardo Rendón-Hernández, Erika Alarcón-Chavira, and Manuel Elías-Gutiérrez. "DNA Barcodes Applied to a Rapid Baseline Construction in Biodiversity Monitoring for the Conservation of Aquatic Ecosystems in the Sian Ka’an Reserve (Mexico) and Adjacent Areas." Diversity 13, no. 7 (2021): 292. http://dx.doi.org/10.3390/d13070292.

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This study is focused on the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied recently developed protocols for the rapid assessment of most animal taxa inhabiting any freshwater system using light traps and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens comprising mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 barcode index numbers (BINs) were detected. From them, we identified 43 species. All others

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Bezeng, B. S., T. J. Davies, B. H. Daru, et al. "Ten years of barcoding at the African Centre for DNA Barcoding." Genome 60, no. 7 (2017): 629–38. http://dx.doi.org/10.1139/gen-2016-0198.

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The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of t

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Li, Qiang, Jun Deng, Cui Chen, et al. "DNA Barcoding Subtropical Aphids and Implications for Population Differentiation." Insects 11, no. 1 (2019): 11. http://dx.doi.org/10.3390/insects11010011.

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DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, represen

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Marquisseau, Anaïs, Kamila Canale-Tabet, Emmanuelle Labarthe, et al. "Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France." Biodiversity Data Journal 13 (January 7, 2025): e137540. https://doi.org/10.3897/BDJ.12.e137540.

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DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for. The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer

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Epitashvili, Giorgi, Matthias Geiger, Jonas Astrin, Fabian Herder, Bella Japoshvili, and Levan Mumladze. "Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia." Biodiversity Data Journal 8 (October 23, 2020): e57862. https://doi.org/10.3897/BDJ.8.e57862.

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In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea bas

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Trébeau, Céline, Jacques Boutet de Monvel, Fabienne Wong Jun Tai, Christine Petit, and Raphaël Etournay. "DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments." Bioinformatics 35, no. 15 (2018): 2690–91. http://dx.doi.org/10.1093/bioinformatics/bty1030.

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Abstract Summary Using adequate DNA barcodes is essential to unambiguously identify each DNA library within a multiplexed set of libraries sequenced using next-generation sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one to design single or dual-barcoding multiplex experiments by imposing desired constraints on the barcodes (including sequencer chemistry, barcode pairwise minimal distance and nucleotide content), while optimizing barcode frequency usage, thereby allowing one to both facilitate the demultiplexing step and spare expensive library-preparation kits. Th

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Pešić, Vladimir, Andrzej Zawal, Ana Manović, Aleksandra Bańkowska, and Milica Jovanović. "A DNA barcode library for the water mites of Montenegro." Biodiversity Data Journal 9 (December 20, 2021): e78311. https://doi.org/10.3897/BDJ.9.e78311.

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Water mites (Acari, Hydrachnidia) are a significant component of freshwater ecosystems inhabiting a wide range of aquatic habitats. This study provides a first comprehensive DNA barcode library for the water mites of Montenegro. DNA barcodes were analysed from 233 specimens of water mites morphologically assigned to 86 species from 28 genera and 15 families. In the course of the study, four species, i.e. <i>Lebertia reticulata</i> (Koenike, 1919), <i>Atractides inflatipalpis</i> K.Viets, 1950, <i>A. latipes</i> (Szalay, 1935) and <i>Parabrachypoda montii</i> (Maglio, 1924) were molecularly con

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Schmid-Egger, Christian, Stefan Schmidt, Paolo Rosa, and Oliver Niehuis. "DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species." Insects 15, no. 11 (2024): 850. http://dx.doi.org/10.3390/insects15110850.

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Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and the discovery of cryptic species difficult to identify based on external morphology have made the identification of several species a challenge. COI barcoding has been instrumental in the identification of some cuckoo wasp species and could help alleviate some of the above problems, but a reliable large reference database containing the cuckoo wasp barcodes is lacking. We present the COI barcodes of more than 800 specimens o

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Jafari, Samin, Björn Müller, Björn Rulik, Vera Rduch, and Peters Ralph S. "Another crack in the Dark Taxa wall: a custom DNA barcoding protocol for the species-rich and common Eurytomidae (Hymenoptera, Chalcidoidea)." Biodiversity Data Journal 11 (May 9, 2023): e101998. https://doi.org/10.3897/BDJ.11.e101998.

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DNA barcodes are a great tool for accelerated species identification and for complementing species delimitation. Furthermore, DNA barcode reference libraries are the decisive backbone feature for any metabarcoding study in biodiversity monitoring, conservation or ecology. However, in some taxa, DNA barcodes cannot be generated with published primers at a satisfying success rate and these groups will consequently be largely missing from any barcoding-based species list. Here, we provide a custom DNA barcoding forward primer for the Eurytomidae (Hymenoptera, Chalcidoidea), elevating the success

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Denissen, Geke A. W., Liza N. van Steenbergen, Wouter T. Lollinga, Nico J. J. Verdonschot, Berend W. Schreurs, and Rob G. H. H. Nelissen. "Generic implant classification enables comparison across implant designs: the Dutch Arthroplasty Register implant library." EFORT Open Reviews 4, no. 6 (2019): 344–50. http://dx.doi.org/10.1302/2058-5241.4.180063.

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In the Dutch Arthroplasty Register (LROI), the product and batch number of prosthetic components and cement are registered for traceability. Registration of the product number provides opportunities to extend the information about a specific prosthesis. All product numbers used from the beginning of the registration in 2007 were characterized to develop and maintain an implant library. The Scientific Advisory Board developed a core-set that contains the most important characteristics needed to form an implant library. The final core-set contains the brand name, type, coating and material of th

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Ušanović, Lejla, Dalila Destanović, Lejla Lasić, Jasna Hanjalić Kurtović, Filipe O. Costa, and Belma Kalamujić Stroil. "Status of the BOLD reference library of DNA barcodes of caddisflies (Insecta: Trichoptera) from the Western Balkans." Periodicum Biologorum 124, no. 3-4 (2023): 107–14. http://dx.doi.org/10.18054/pb.v124i3-4.24754.

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Background and purpose: Available data in research literature suggest that the Western Balkan countries hold a rich diversity of caddisflies. Assessment and biomonitoring of such rich diversity could be facilitated through DNA-based high-throughput approaches like DNA metabarcoding that depend on the availability of comprehensive reference libraries. Materials and methods: We assessed the status of the COI barcode sequence data for a total of 112 caddisflies species in the investigated region by determining the gaps in representative sequences in the Barcode of Life Data System (BOLD) and exam

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Choudhury, Subhendu Roy, Shixiong Wang, Yevhen Akimov, et al. "Abstract 5544: Identification, isolation and molecular characterization of drug-resistant sub-populations of pancreatic cancer cells." Cancer Research 85, no. 8_Supplement_1 (2025): 5544. https://doi.org/10.1158/1538-7445.am2025-5544.

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Abstract Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, since most PDAC tumors develop resistance to the standard of care (SoC) treatments like chemotherapy, radiation, and targeted therapies. All tumors consist of multiple, genetically related subpopulations of cancer cells that evolve in parallel and display heterogeneity at genomic, epigenetic, or phenotypic levels. As cancer develops, some subpopulations of cancer cells may show faster growth, increased metastatic potential, and resistance toward SoC treatment. A key challenge in PDAC management is understanding chemoresista

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Gadawski, Piotr, Bruno Rossaro, Wojciech Giłka, et al. "DNA barcode library revealed unknown diversity of chironomid midges in Montenegro." ARPHA Conference Abstracts 4 (March 4, 2021): e65497. https://doi.org/10.3897/aca.4.e65497.

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We present the first results of the study aiming to investigate the diversity of the non-biting midges (Diptera: Chironomidae) fauna of the Skadar Lake system (Montenegro and Albania), a well-known hotspot of freshwater biodiversity composed by the young lake Skadar (originated 1200 before present) and by its old system of springs (originated during Pliocene). During the study, 8,147 COI barcodes were obtained and revealed the presence of 474 BINs and 586 OTUs assigned to 148 species. Our results provide the first insight into the factual molecular diversity among chironomids inhabiting Skadar

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Levesque-Beaudin, Valerie, Meredith Miller, Torsten Dikow, et al. "A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections." Biodiversity Data Journal 11 (May 10, 2023): e100677. https://doi.org/10.3897/BDJ.11.e100677.

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Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society – through, for example, digitisation or the construction of a validated, global DNA barcode library – is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging,

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Jamdade, Rahul, Maulik Upadhyay, Khawla Al Shaer, et al. "Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification." Plants 10, no. 12 (2021): 2741. http://dx.doi.org/10.3390/plants10122741.

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Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers’ reliability. Our analysis suggests that from the unsupervised method,

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