Author: Sabath, Niv; Wagner, Andreas; Karlin, David
Title: Evolution of Viral Proteins Originated De Novo by Overprinting Document date: 2012_7_19
ID: 629fwmgk_43
Snippet: We extracted all fully sequenced viral genomes from the NCBI viral genome database (Bao et al. 2004) in June 2011 and identified all viral proteins annotated in these genomes. All homology searches were carried out against a database of these proteins, using PSI-basic local alignment search tool (BLAST) (Altschul et al. 1997) with an E value cutoff of 10 À6 . We performed all multiple sequence alignments using MAFFT (Katoh et al. 2002) and const.....
Document: We extracted all fully sequenced viral genomes from the NCBI viral genome database (Bao et al. 2004) in June 2011 and identified all viral proteins annotated in these genomes. All homology searches were carried out against a database of these proteins, using PSI-basic local alignment search tool (BLAST) (Altschul et al. 1997) with an E value cutoff of 10 À6 . We performed all multiple sequence alignments using MAFFT (Katoh et al. 2002) and constructed phylogenetic trees with the BIONG method (Gascuel 1997) . We rooted these trees with the mid-point rooting method (Farris 1972) . We predicted the domain organization of proteins encoded by overlapping genes using ANNIE (Ooi et al. 2009 ).
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