PubMed · 11808743
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P T Spellman. 2001. The future of publishing microarray data.. https://doi.org/10.1093/bib%2F2.4.316
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Members of the International Nucleotide Sequence Database Collaboration (INSDC; https://www.insdc.org/) collect, exchange, and preserve comprehensive open nucleotide sequence information and provide tools for its access. The INSDC has stated its commitment to welcoming new members into the collaboration to be more representative of the global community of data and users. To reach this goal, a comprehensive definition of the INSDC data model and minimum requirements for data acceptance have been established. Here we describe the processes used to arrive upon these INSDC Specifications and lay out strategies for their continued upkeep to remain current and relevant. Database URL:  https://www.insdc.org/.
GenBank contains 4879 expressed sequence tags (EST) derived from four non-normalized human ovarian cDNA libraries. Of these EST, 2646 are contributors to UniGene clusters and have UniGene numbers. The EST map to 1206 distinct UniGenes. A gene expression profile was established for the human ovary by identifying the abundance of each UniGene cluster and its corresponding annotation. The most highly expressed transcripts were for proteins associated with protein synthesis (ribosomal proteins, elongation factors, thymosins, etc.). However, there are also transcripts for genes of unknown function that are ovary-specific. This ovarian gene expression profile provides useful data for the design of DNA microarrays targeted at ovarian function and highlights novel sequences that warrant further investigation.
Most HIV-1 infections in Uganda are caused by subtypes A and D. The prevalence of recombination and the sites of specific breakpoints between these subtypes have not been reported. HIV-1 pol sequences encoding protease (amino acids 1-99) and reverse transcriptase (amino acids 1-324) from 102 pregnant Ugandan women were analyzed by the Recombinant Identification Program, SimPlot, and examination of phylogenetically informative sites to identify sites of recombination between sequence segments belonging to different subtypes. Thirteen percent (13 of 102) of the pol sequences contained strong evidence of recombination between subtypes A and D. At least nine different patterns of recombination were observed. Five women infected with a recombinant virus transmitted the recombinant virus perinatally. In this population-based study, intersubtype recombinants were common. The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability.