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_32
Snippet: Each complete sequence S is aligned to the covariance model for M (S) using Infernal's cmalign program generating a Stockholm formatted alignment file. The alignment is then parsed to determine a mapping between sequence positions and model positions, from which per-feature coordinates for S are derived. The cmalign output Stockholm alignment file includes posterior probability values that indicate a level of confidence in each aligned nucleotide.....
Document: Each complete sequence S is aligned to the covariance model for M (S) using Infernal's cmalign program generating a Stockholm formatted alignment file. The alignment is then parsed to determine a mapping between sequence positions and model positions, from which per-feature coordinates for S are derived. The cmalign output Stockholm alignment file includes posterior probability values that indicate a level of confidence in each aligned nucleotide. These posterior probability values are used to identify features for which the endpoints are not confidently assigned by the model, which are reported as fatal alerts (indf5loc and indf3loc). Different fatal alerts are reported if an input sequence has a gap at a feature endpoint (indf5gap or indf3loc). Additional alerts are potentially reported at this stage as well (Table 3) .
Search related documents:
Co phrase search for related documents- alignment file and format alignment file: 1
- cmalign program and covariance model: 1
- cmalign program and input sequence: 1
- complete sequence and input sequence: 1
- covariance model and input sequence: 1, 2, 3
Co phrase search for related documents, hyperlinks ordered by date