Selected article for: "GenBank accession and GitHub repository"
Author: Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga
Title: Capturing diverse microbial sequence with comprehensive and scalable probe design
  • Document date: 2018_3_12
    • ID: a9lkhayg_96
    Snippet: Sequences used as input for probe design (Supplementary Table 1 ) are available in the repository at https://github.com/broadinstitute/catch. Sequences of the probe designs are available at https://github.com/broadinstitute/catch/tree/cf500c6/probe-designs. Viral genomes sequenced as part of this study will be deposited in NCBI GenBank 36 prior to publication under BioProject accession PRJNA431306 (PRJNA436552 for the 2018 Lassa virus genomes). F.....
    Document: Sequences used as input for probe design (Supplementary Table 1 ) are available in the repository at https://github.com/broadinstitute/catch. Sequences of the probe designs are available at https://github.com/broadinstitute/catch/tree/cf500c6/probe-designs. Viral genomes sequenced as part of this study will be deposited in NCBI GenBank 36 prior to publication under BioProject accession PRJNA431306 (PRJNA436552 for the 2018 Lassa virus genomes). Figure 1 -Parameters used by CATCH in default model of hybridization. CATCH models hybridization between each possible candidate probe and the target sequences. Doing so allows CATCH to decide whether a candidate probe captures (or "covers") a region of the target sequence, and thus find a probe set that achieves a desired coverage of the target sequences under this model. For whole genome enrichment, the desired coverage would typically be 100% of each target sequence. (a) Relatively conserved regions (e.g., a particular gene) in the input sequences can be captured with few probes because it is likely that any given probe, under a model of hybridization, will capture observed variation across many or all of the input sequences. Highly variable regions may require many probes to be captured because each given probe may capture the observed variation across only a small fraction of the input sequences. (b) By default, CATCH decides whether a probe hybridizes to a region of a target sequence according to the following parameters: a number m of mismatches to tolerate and a length lcf of a longest common substring. CATCH computes the longest common substring with at most m mismatches between the probe and target subsequence, and decides that the probe hybridizes to the target if and only if the length of this is at least lcf. If the parameter i is provided, CATCH additionally requires that the probe and target subsequence share an exact (0-mismatch) match of length at least i. If CATCH decides that the probe hybridizes to the subsequence of the target with which it shares a substring, then it determines that the probe captures the region equal to the length of the probe as well as e nt on each side of this region. e, termed a cover extension, is a parameter whose value is specified to CATCH, along with m, lcf, and i.

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