Author: Franzo, Giovanni; Cecchinato, Mattia; Tosi, Giovanni; Fiorentini, Laura; Faccin, Francesca; Tucciarone, Claudia Maria; Trogu, Tiziana; Barbieri, Ilaria; Massi, Paola; Moreno, Ana
Title: GI-16 lineage (624/I or Q1), there and back again: The history of one of the major threats for poultry farming of our era Document date: 2018_12_20
ID: 0pi042qi_3
Snippet: International database preparation. To download all available IBV sequences overlapping with the region of interest (HVR3), one of the Italian sequences was used as query in BLAST and all sequences with a genetic distance lower than 30% were downloaded. Obtained sequences plus the Italian ones were merged with the reference set provided by Valastro et al., [6] and aligned using MAFFT [26] . Partial sequences (i.e. covering only part of the HVR3) .....
Document: International database preparation. To download all available IBV sequences overlapping with the region of interest (HVR3), one of the Italian sequences was used as query in BLAST and all sequences with a genetic distance lower than 30% were downloaded. Obtained sequences plus the Italian ones were merged with the reference set provided by Valastro et al., [6] and aligned using MAFFT [26] . Partial sequences (i.e. covering only part of the HVR3) and those with unknown nucleotides, frameshift mutations and premature stop codons, suggestive of poor sequence quality, were removed from the dataset.
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