29 Matching Annotations
  1. Nov 2022
    1. Detailed descriptions, assumptions, limitations and test cases of many popular statistical methods for ecological research can be found in the GUSTAME server (Buttigieg and Ramette, 2014), and in the review by Paliy and Shankar (2016).
    2. The advantages of using SSU rRNA for community fingerprinting are many: (i) This gene is found in all cellular life forms. (ii) It is a highly conserved gene, serving to a large degree as a reliable molecular chronometer. (iii) It is seldom transferred horizontally. (iv) It possesses both conserved and variable regions, so that the conserved regions can be targeted by polymerase chain reaction (PCR) primers and the variable ones be used as identifying markers. A handful of other genes, such as the large subunit (LSU) rRNA share these properties, but the length of ~1,500 bp of the bacterial SSU rRNA made it amenable to early molecular techniques, and the impressive body of knowledge that has since accumulated on the basis of this gene makes a switch to other markers very impractical, except in certain sub-fields such as mycology, where ITS and LSU are widely used.

      very crisp summary

  2. Oct 2022
    1. the majority of chimeras are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence
  3. Aug 2022
    1. The interaction operator strict requires a strict sequencing (order) of the operands on the first level within the combined fragment
    2. The interaction operator seq means that the combined fragment represents a weak sequencing between the behaviors of the operands.
    3. Weak sequencing reduces to a parallel merge when the operands are on different sets of participants. Weak sequencing reduces to strict sequencing when the operands work on the same participant.

      weak sequencing - reduces to: - or: - parallel (simultaneous) - strict sequencing

  4. May 2022
    1. For background information on how tiling amplicon sequencing works, please prefer to the original “PrimalSeq” protocol paper as tested on Zika Quick et al. Nature Protocols and a follow-up paper Grubaugh, Gangavaparu et al. Genome Biology that focuses on in-host variation and Illumina sequencing.
  5. Jan 2022
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  10. Aug 2020
    1. Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510

  11. Jul 2020
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  14. Jan 2020
    1. OCTOPUS, a light-weight, cost-effective, and robust method for full-plasmid sequence verification using next-generation sequencing
  15. Mar 2018
  16. Nov 2017
    1. Comparison of SNVs detected in the whole genome sequencing data with SNPs genotyped using arrays

      inference of "%diploid coverage"