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1.
  • Haas, Brian J., et al. (författare)
  • De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
  • 2013
  • Ingår i: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 8:8, s. 1494-1512
  • Tidskriftsartikel (refereegranskat)abstract
    • De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
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2.
  • Rivas-Carrillo, Salvador Daniel, et al. (författare)
  • Broad-scale in silico assessment retroviral exaptated gene : syncytin
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Syncytin is a fossil protein exapted from retroviruses that fulfills a pivotal role during trophoblast implantation and placental metabolite exchange. However, little is yet known about the distribution of syncytin across vertebrates. Here, we searched a library of more than 150 high-quality assemblies across 17 taxonomical orders for syncytin homologs. We identified and syntenically aligned over 300 loci insertions, including not previously known insertions. Additionally, we predicted the tridimensional structures of the recover sequences using AlphaFold2. Sequence conservation and phylogenomics analyses suggest a complex dynamic of multiple retroviral insertions at different time points with sequence conservation specific to clades that share a similar histo-physiological placental type. This research has widened our knowledge about the physiology of placentation through a better understanding of the evolutionary role of syncytin.
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