Selected article for: "default library and input sequence"
Author: Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki
Title: VADR: validation and annotation of virus sequence submissions to GenBank
  • Document date: 2019_11_22
    • ID: besvz92f_26
    Snippet: Each v-annotate.pl input query sequence is first scored against each model in the library, which by default is the VADR v1.0 library of 194 models. The comparison is made between HMMs from the CM file and each sequence using an abbreviated version of the HM-MER3 [17, 18] filter pipeline as implemented in Infernal v1.1.3 [19] . The full HMMER3 pipeline includes more than five stages, but only the first three stages are carried out during this clas.....
    Document: Each v-annotate.pl input query sequence is first scored against each model in the library, which by default is the VADR v1.0 library of 194 models. The comparison is made between HMMs from the CM file and each sequence using an abbreviated version of the HM-MER3 [17, 18] filter pipeline as implemented in Infernal v1.1.3 [19] . The full HMMER3 pipeline includes more than five stages, but only the first three stages are carried out during this classification stage of vannotate.pl, which computes a local forward score of a window of the input sequence. The window boundaries reported at this stage of the filter pipeline are inexact but this imprecision is irrelevant for the classification This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.

    Search related documents:
    Co phrase search for related documents
    • CC0 license and Government work: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • classification stage and filter pipeline: 1
    • classification stage and Government work: 1, 2
    • classification stage and input sequence: 1
    • CM file and input sequence: 1, 2
    • CM file and library model: 1
    • filter pipeline and input sequence: 1
    • input query sequence and query sequence: 1
    • input sequence and library model: 1, 2
    • input sequence and query sequence: 1, 2, 3