Selected article for: "GenBank file and genome GenBank file"
Author: Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris
Title: Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome
  • Document date: 2006_6_13
    • ID: 1e2kkhht_29
    Snippet: For our second test using bacterial genomes, we used two different species from the Thermoplasma genus; T. volcanium strain GSS1 (NC_002689) was annotated using T. acidophilum strain DSM 1728 (NC_002578) as a reference. The reference genome GenBank file contained 1482 annotated genes, and based on a threshold of 60% aa similarity 1103annotations (74%) were accepted automatically into the target genome annotation (11 genes had 100% similarity, 135.....
    Document: For our second test using bacterial genomes, we used two different species from the Thermoplasma genus; T. volcanium strain GSS1 (NC_002689) was annotated using T. acidophilum strain DSM 1728 (NC_002578) as a reference. The reference genome GenBank file contained 1482 annotated genes, and based on a threshold of 60% aa similarity 1103annotations (74%) were accepted automatically into the target genome annotation (11 genes had 100% similarity, 135 genes were 95-100% similar, 182 genes were 90-94% similar, 164 genes were 85-89% similar, 186 genes were 80-84% similar, 141 genes were 75-79% similar. 120 genes were 70-74% similar and 459 genes were <70% similar. A further 124 ORFs could be added from the Unassigned-ORFs table; most of these ORFs were truncated and/or fragmented versions of their counterparts in the reference genome. Finally, a number of target genome-specific ORFs (201) were added following further analysis of the Unassigned-ORFs, to yield a total of 1428 ORFs accepted for annotation. A comparison between our annotation of GSS1 using GATU and the annotated GSS1 GenBank file (NC_002689) showed 100 differences, approximately 7% [see Additional file 2].

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