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. 2013 Nov 27;42(Database issue):D222–D230. doi: 10.1093/nar/gkt1223

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© The Author(s) 2013. Published by Oxford University Press.

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Figure 2. — Results from searching Pfam with the Hepatitis B virus isolate G376-7, complete genome (GenBank accession AF384371.1), providing a striking example of overlapping genes. The six reading frames are displayed graphically in the top box of the results page. All three reading frames from the positive strand contain matches to Pfam-A, which are tabulated below. The positions of stop codons are indicated by the square lollipops. The results are shown with the ‘protein’ coordinates of the open reading frame, but it is also possible to toggle this to DNA sequence coordinates. This search tool accepts sequences up to 80 000 nucleotides in length, and searches the Pfam-A HMM library using the gathering threshold.