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_84
Snippet: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/852657 doi: bioRxiv preprint secondary structure are essentially equivalent models. However, we opted to always use CMs for the alignment stage because the popular HMM package HM-MER3 is not well-suited to accurately defining alignment endpoints, as it is restricted to local alignment only, whereas Infernal allows global alignment .....
Document: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/852657 doi: bioRxiv preprint secondary structure are essentially equivalent models. However, we opted to always use CMs for the alignment stage because the popular HMM package HM-MER3 is not well-suited to accurately defining alignment endpoints, as it is restricted to local alignment only, whereas Infernal allows global alignment with respect to the sequence, and consequently can identify at least some boundaries more accurately.
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