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Relevant bibliographies by topics / Sequence submission

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Academic literature on the topic 'Sequence submission'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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Journal articles on the topic "Sequence submission"

1

Gruenstaeudl, Michael. "annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA." Bioinformatics 36, no. 12 (2020): 3841–48. http://dx.doi.org/10.1093/bioinformatics/btaa209.

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Abstract Motivation The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions. Results The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-sca

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Wong, Mark, and Rhodri Leng. "On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa." F1000Research 8 (July 26, 2019): 1200. http://dx.doi.org/10.12688/f1000research.18656.1.

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This paper describes a unique two-step methodology used to construct six linked bibliometric datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. First, we retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first linked to these sequence lengths in the scientific literature. For each species, this resulted in two associated datasets: 1) A .csv f

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Wong, Mark, and Rhodri Leng. "On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa." F1000Research 8 (October 23, 2020): 1200. http://dx.doi.org/10.12688/f1000research.18656.2.

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This paper describes a unique two-step methodology used to construct six linked bibliometric datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. First, we retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first linked to these sequence lengths in the scientific literature. For each species, this resulted in two associated datasets: 1) A .csv f

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Griffin, Hugh G., and Annette M. Griffia. "WWW Nucleotide sequence submission System." Molecular Biotechnology 5, no. 1 (1996): 71. http://dx.doi.org/10.1007/bf02762417.

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Wong, Mark, and Rhodri Leng. "On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa." F1000Research 8 (February 28, 2023): 1200. http://dx.doi.org/10.12688/f1000research.18656.3.

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This data note describes a unique two-step methodology to construct six linked datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. The datasets were used as evidence in a project that investigated the history of genomic science. To design the datasets, we first retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each of our three species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first described thes

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Levy, Richard, Jessie Berta-Thompson, Gary Olds, and Andrew Wilson. "Specimods: A web-based tool for producing Genbank submission files for sequenced museum specimens." Biodiversity Information Science and Standards 6 (September 9, 2022): e94596. https://doi.org/10.3897/biss.6.94596.

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The expectation of published sequence data on Genbank and other sequence databases is not only a requirement for journal publication, but is incredibly valuable for continuing research in organismal evolution and ecology. The process of formatting and submitting sequence data from vouchered specimens is burdensome and tedious. Improperly formatted submissions lead to lengthy delays and frustrations on behalf of the submitters and reviewers. Specimods*1 is a new tool that utilizes the Global Biodiversity Information Facility (GBIF) API to produce formatted source modifier files that will facili

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Leng, Rhodri, Gil Viry, Miguel García-Sancho, James Lowe, Mark Wong, and Niki Vermeulen. "The Sequences and the Sequencers." Historical Studies in the Natural Sciences 52, no. 3 (2022): 277–319. http://dx.doi.org/10.1525/hsns.2022.52.3.277.

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This special issue on sequences and sequencers uses new analytical approaches to re-assess the history of genomics. Historical attention has largely focused on a few central characters and institutions: those that participated in the Human Genome Project (HGP), especially its final stages. Our analysis—based on an assessment of almost 13.5 million DNA sequence submissions and 30,000 publications of human, yeast, and pig DNA sequences—followed overlapping chronologies starting before and finishing after the concerted efforts to sequence the genomes of each species: 1980 to 2000 in yeast, 1985 t

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Gilna, P., L. J. Tomlinson, and C. Burks. "Submission of Nucleotide Sequence Data to GenBank(R)." Microbiology 135, no. 7 (1989): 1779–86. http://dx.doi.org/10.1099/00221287-135-7-1779.

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Tuli, Mary Ann, Tomas P. Flores, and Graham N. Cameron. "Submission of nucleotide sequence data to EMBL/GenBank/DDBJ." Molecular Biotechnology 6, no. 1 (1996): 47–51. http://dx.doi.org/10.1007/bf02762322.

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Shadek, Teuku Fadjar, Shodik Nuryadhin, and Ainin Najmi. "PENGEMBANGAN SISTEM PENGAJUAN UTTP DENGAN MENGGUNAKAN PROGRAM BOOTSTRAP (PHP) DALAM RANGKA PENINGKATAN DAYA SAING DAN INOVASI PADA PT KALIBRASI INDONESIA MANDIRI." Jurnal Sistem Informasi dan Informatika (Simika) 6, no. 1 (2023): 69–79. http://dx.doi.org/10.47080/simika.v6i1.2361.

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PT Kalibrasi Indonesia Mandiri is one unit of the legal metrology agency in Serang Regency that functions are to control, manage and determine the types of measuring instruments, scales and equipment (UTTP) by setting mass standards, volume standards and length standards. PT Kalibrasi Indonesia Mandiri is under department of Industry, Trade, Cooperatives and SMEs in Banten province, as one of the Technical Implementation Unit (UPT). In accepting UTTP (Measuring, Measure, Weighing, and Equipment) submissions from institutions or companies is still manual and there is no system. For this reasons

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Book chapters on the topic "Sequence submission"

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Rice, Catherine M., and Graham N. "Submission of Nucleotide Sequence Data to EMBIVGenBank/DDB J." In Computer Analysis of Sequence Data. Humana Press, 1994. http://dx.doi.org/10.1385/0-89603-276-0:413.

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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes. CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a

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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes. CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0015.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a

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Underwood, Anthony P., William Bellamy, Baharak Afshar, Norman K. Fry, and Timothy G. Harrison. "Development of an Online Tool for European Working Group for Legionella Infections Sequence-Based Typing, Including Automatic Quality Assessment and Data Submission." In Legionella. ASM Press, 2014. http://dx.doi.org/10.1128/9781555815660.ch44.

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"XML for INSD sequence submission." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_18266.

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Sharma, Rupali, Shashwat Sharad, Gillipsie Minhas, Deep Raj Sharma, Kulsajan Bhatia, and Neel Kamal Sharma. "DNA, RNA isolation, primer designing, sequence submission, and phylogenetic analysis." In Basic Biotechniques for Bioprocess and Bioentrepreneurship. Elsevier, 2023. http://dx.doi.org/10.1016/b978-0-12-816109-8.00012-x.

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Spallone, Roberta. "Digital Animation for Representing Architectural Design." In Advances in Environmental Engineering and Green Technologies. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7359-3.ch004.

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Since the late nineties digital movies have emerged as one of the main methods for submission of architectural designs at international competitions, public presentations, and shares on websites of contemporary masters. The chapter highlights how the ability to access the fourth dimension, through the construction of a sequence of images, constitutes a specific prerogative of digital representation, which goes beyond the static constraint imposed by conventional methods of representation. The author investigates the methods, techniques, and languages of the fourth-dimensional communication of

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Spallone, Roberta. "Digital Animation for Representing Architectural Design." In Encyclopedia of Information Science and Technology, Fourth Edition. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-2255-3.ch084.

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Since the late Nineties digital movies are emerging as one of the main methods for submission of architectural designs at international competitions, public presentations and shares on websites of contemporary masters. The chapter highlights how the ability to access the fourth dimension, through the construction of a sequence of images, constitutes a specific prerogative of digital representation, which goes beyond the static constraint imposed by conventional methods of representation. The author investigates on the methods, techniques and languages of the fourth-dimensional communication of

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Kirschke, Heidrun, Alan J. Barrett, and Neil D. Rawlings. "Cathepsin K (EC 3.4.22.38)." In Lysosmal Cysteine Proteases. Oxford University PressOxford, 1998. http://dx.doi.org/10.1093/oso/9780198502494.003.0006.

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Abstract peptidase named OC-2. In the same year, human equivalents of the rabbit gene were mentioned independently in two abstracts by Drake et al. [1787] and Li et al. [1797] and the sequence was published in 1995 (in order of date of submission) by Li et al. [ 1798], lnaoka et al. [1792], Shi et al. [1811] and Br6mme and Okamoto [1780]. The cDNA of cathepsin K from mouse [1642, 1806] and chicken [1520] have also been cloned. Names such as cathepsin X [1798], cathepsin K [1792], cathepsin O [1811, 1760, 1643] and cathepsin 02 [1780] were given to the novel human osteoclast cysteine peptidase

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Tilmann, Winfried. "Article 57 Court experts." In Unified Patent Protection in Europe: A Commentary. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198755463.003.0105.

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A Court expert provides evidence that may be employed by the Court if its knowledge, including the level of knowledge gained from the evidence produced by the submissions of the parties and the evidence submitted by them, is not sufficient to reach a decision. Legally, it is classed as part of the sequence of all evidence in the case (Art 53(1) UPCA), and does not have a higher status than other evidence available to the Court or the technical explanations provided in the pleadings by the parties or their oral submissions together with demonstrations merely because the evidence of that expert

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Conference papers on the topic "Sequence submission"

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Koblinsky, Bernard W., and Kirk R. Shields. "Unique Design and Award Selection Process (the Re-painting of a 54-Story Building)." In SSPC 2011. SSPC, 2011. https://doi.org/10.5006/s2011-00065.

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Abstract The BNY Mellon faced the considerable challenge of repainting the exterior of the 54-story, metal sided One Mellon Center located in Pittsburgh, Pennsylvania. Located in the heart of the downtown, traditional methods of surface preparation and coating application were not viable options. BNY Mellon took the unusual approach of designing the entire project, from the means and methods, to equipment & staging versus the more traditional process of letting a painting contractor design the work sequence and approach. This work involved creating an internal design team from securing the

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Girrbach, Leander. "SIGMORPHON 2022 Shared Task on Grapheme-to-Phoneme Conversion Submission Description: Sequence Labelling for G2P." In Proceedings of the 20th SIGMORPHON workshop on Computational Research in Phonetics, Phonology, and Morphology. Association for Computational Linguistics, 2023. http://dx.doi.org/10.18653/v1/2023.sigmorphon-1.28.

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Girrbach, Leander. "SIGMORPHON 2022 Shared Task on Morpheme Segmentation Submission Description: Sequence Labelling for Word-Level Morpheme Segmentation." In Proceedings of the 19th SIGMORPHON Workshop on Computational Research in Phonetics, Phonology, and Morphology. Association for Computational Linguistics, 2022. http://dx.doi.org/10.18653/v1/2022.sigmorphon-1.13.

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Kabir, Tasnim, and Marine Carpuat. "The UMD Submission to the Explainable MT Quality Estimation Shared Task: Combining Explanation Models with Sequence Labeling." In Proceedings of the 2nd Workshop on Evaluation and Comparison of NLP Systems. Association for Computational Linguistics, 2021. http://dx.doi.org/10.18653/v1/2021.eval4nlp-1.22.

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Papapetrou, Georghios Dorou, Chia Pei Chuen, Mohd Nur Adzizie Mahamad, Ros Aliza Md Rabi, and Yong Han Seah. "FDP Simulation Studies for Green Fields Cluster Development in Less than 30 Days Utilizing Cloud Technologies." In ADIPEC. SPE, 2022. http://dx.doi.org/10.2118/211415-ms.

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Abstract BD Cluster green fields development located offshore Sabah, Malaysia, consists of three multi-stacked turbidite fields, namely A, B and C, encompassing thick and thin bed sands. Due to the lack of existing infrastructure in close proximity, a wellhead platform (WHP) will be installed on top of Field A. Fields B and C will be developed with a respective 8 and 7km subsea tie back to this WHP. Gas will be exported from the WHP to Facility-1 situated 5km away, whereas oil from a single thin oil rim reservoir in Field A will be exported to Facility-2 50km away. The challenges faced by the

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Li, Yankai, Huan Li, Yingjie Zhu, et al. "Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences." In 2012 Computing, Communications and Applications Conference (ComComAp). IEEE, 2012. http://dx.doi.org/10.1109/comcomap.2012.6154863.

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Burianova, Maria, and Martin Magdin. "PREPARING THE STUDENTS FOR SUCCESSFUL COMPLETION OF UNIVERSITY STUDIES." In eLSE 2015. Carol I National Defence University Publishing House, 2015. http://dx.doi.org/10.12753/2066-026x-15-004.

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The completion of study at the university is marked by passing the state exam, which needs to be defended as part of the final thesis. The state exam verifies the knowledge and skills that the student acquired during their studies and assesses their ability to use these skills in resolving the challenges presented by their field of study. The choice of thesis and their registration to the Academic Information System is ordinarily scheduled for the beginning of the third semester of study. This presents the key questions: Is the student mature enough at the time to be able to choose the right t

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Nosov, Konstantin, and Lubov’ Tarasova. "The Analysis of Activity of the Teacher of Engineering Geometry in the Conditions of the Digital Educational Environment." In 31th International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2021. http://dx.doi.org/10.20948/graphicon-2021-3027-745-753.

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In article some aspects of activity of the teacher of engineering geometry in the conditions of remote work in the digital educational environment are considered. On the example of one of stages of work of the teacher of engineering geometry - check of the individual graphic tasks performed by students, the arising problems connected with "digitalization" of the geometric- graphic training in technical college are discussed. Data on the sequences of actions at the organization of "classical" process of training and training in the digital educational environment are compared and examples of al

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England, Ruth. "36 Complaint implicative sequences in palliative care consultations – an exploratory observational study using conversation analysis." In Accepted Oral and Poster Abstract Submissions, The Palliative Care Congress, Sustaining Each Other, Growing Together, 16–17 March 2023, The Edinburgh International Conference Centre (EICC), Edinburgh, Scotland. British Medical Journal Publishing Group, 2023. http://dx.doi.org/10.1136/spcare-2023-pcc.56.

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Gomes, Ana Luiza de Freitas Magalhães, Letícia da Conceição Braga, Paulo Guilherme de Oliveira Salles, Carolina Pereira de Souza Melo, and Clécio Ênio Murta de Lucena. "Mutations in the FANCC and CREBBP genes differentiate a case of a patient with triple-negative breast tumor and favorable clinical progression." In XXVI Brazilian Mastology Congress. Mastology, 2024. https://doi.org/10.29289/259453942024v34s2003.

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Introduction: Triple-negative breast cancer (TNBC) accounts for approximately 15% of diagnosed cases. Characterized by the lack of tumor expression of estrogen, progesterone, and HER2 receptors, it is the most aggressive subtype with the poorest prognosis, exhibiting heterogeneous behavior given the limited available systemic therapies. The heterogeneity of TNBC was first studied by Lehmann et al. in 2011, and with ongoing research, the disease is now divided into five distinct groups: basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), luminal androgen receptor-positive (LAR), and

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