Preserving Accuracy in GenBank

Molecular Biotechnology, 1999

Systematic Biology, 2008

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.

ZooKeys, 2013

Trends in Ecology and Evolution, 2003

Taxonomy underpins all biological research, with implications for many basic scientific and applied fields. Insights into the stability or change of animal and plant guilds require species identification on a broad scale and biodiversity questions have become a major public issue. But this comes at a time when taxonomy is facing a crisis, because ever fewer specialists are available. Here, we explore the possibility of using DNA-based methodology to overcome these problems. The utility of DNA sequences for taxonomic purposes is well established. However, all current taxonomic approaches intend to use DNA, at best, as an auxiliary criterion for identifying a species or a taxon, but have not given it a central role. We propose a scheme in which DNA would be the scaffold of a taxonomic reference system, whilst maintaining the importance of the morphological information associated with whole specimens.

Nucleic Acids Research, 2004

The ARB (arbor, latin: tree) project was initiated almost ten years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data it can also be used for any nucleic and amino acid sequence data. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or world wide network. A phylogenetic tree visualised in the main window can be used for data access and visualisation. The package comprises of furthermore tools for data im-and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridisation probe design and evaluation and other components for data analysis. Currently, the package is more used by the scientific community all over the world.

Systematic and Applied Microbiology, 2013

High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.

Puji syukur penulis panjatkan kehadirat Tuhan Yang Maha Esa atas rahmat dan hidayahnya, sehingga kelompok dapat menyelesaikan makalah ini yang berjudul "EPIDEMIOLOGI PENYAKIT HIPERTENSI" Pembuatan makalah ini, tidak lepas dari dan bantuan dari berbagai pihak. Oleh karena itu, pada kesempatan ini kelompok menyampaikan sebuah ucapan terima kasih kepada pihak atau sumber yang telah membantu dalam pembuatan makalah ini.

Zweite Natur. . Julia Christ und Axel Honneth (hrsg), 2019

In a footnote to *Mind and World*, John McDowell writes: "Even those aspects of mature human life that are shaped by *Bildung* show unassimilated residues of first nature. This is a way of putting a central thought of Freud." I argue that Freud's view is more radical than McDowell's formulation suggests. What McDowell calls "first nature" is not a mere residue but a permanent feature of adult human life. Moreover, Freud's account of primary and secondary mental processes puts pressure on John McDowell's distinction between first and second nature, for primary processes seem to belong, strictly speaking, to neither "first" nor "second" nature, on McDowell's definition of those concepts. The paper attempts to locate Freud's view in comparison with the Kantian and Hegelian views to which McDowell more often refers in characterizing his own.

Pembagian hukum kedalam hukum publik dan hukum privat yang dilakukan oleh ahli hukum romawi, ulpianus, ketika ia menlis "publicum ius est, quod ad statum rei romanea spectat, privatum quod ad singulorum utitilatem " (hukum publik adalah hukum yang berkenaan dengan kesejahteraan negara romawi, sedangkan hukum privat adalah hukum yang mengatur hubungan kekeluargaan), pengaruhnya cukup besar dalam sejarah pemikiran hukum, sampai sekarang. Pergaulan hukum (rechtsverkeer), badan hukum (rechtsperson).