Author: Wang, Shiliang; Sundaram, Jaideep P; Spiro, David
Title: VIGOR, an annotation program for small viral genomes Document date: 2010_9_7
ID: 0lbxvudt_32
Snippet: The influenza sequence set was also run through FLAN (influenza specific gene prediction program). The specificity and sensitivity of FLAN are quite comparable to VIGOR (Table 1) . However, 47 genes annotated in GenBank were predicted as non-functional genes by FLAN because of different problems detected in these sequences including internal stop codons, frame shifts or incorrect splicing. These predictions were marked as discrepancies in Table 1.....
Document: The influenza sequence set was also run through FLAN (influenza specific gene prediction program). The specificity and sensitivity of FLAN are quite comparable to VIGOR (Table 1) . However, 47 genes annotated in GenBank were predicted as non-functional genes by FLAN because of different problems detected in these sequences including internal stop codons, frame shifts or incorrect splicing. These predictions were marked as discrepancies in Table 1 . Nine small ORFs detected by FLAN were missing from the VIGOR prediction list; all of these were homologous to PB1-F2 protein. These PB1-F2 proteins predicted by FLAN were manually compared to the homologous PB1-F2 sequences. It was found that multiple stop codons are present in the region homologous to the N-terminal domain of PB1-F2. Although the annotations in GenBank for 6 of these nine sequences are same as FLAN predictions, most likely all these nine sequences encode non-functional PB1-F2 genes.
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