PMC:4502366 / 8186-9173 JSONTXT

{"project":"2_test","denotations":[{"id":"25911226-22982435-43388783","span":{"begin":112,"end":116},"obj":"22982435"},{"id":"25911226-22139921-43388784","span":{"begin":244,"end":248},"obj":"22139921"},{"id":"25911226-18033792-43388785","span":{"begin":427,"end":431},"obj":"18033792"}],"text":"Annotation\nThe T. rathkei mitochondrial genome was initially annotated using the MITOS web server (Bernt et al. 2013), which identifies protein-coding and rRNA genes using homology searches, and a variant of the MITFI algorithm (Juhling et al. 2012) to identify putative tRNA genes. We used the invertebrate mitochondrial genetic code, and the default settings for all other parameters. We also used ARWEN (Laslett and Canback 2008) to provide a complementary set of predicted tRNA genes. Finally, the annotations for the protein-coding and rRNA were manually corrected, aided by BLAST searches against other isopod mitochondrial genes, because in many cases the initial sequences generated by the automated software lacked start or stop codons or were obviously incomplete (e.g., rRNA genes were too short). The C. convexus mitochondrial genome was annotated similarly, using BLAST searches to identify protein-coding and ribosomal RNA genes, and MITFI and ARWEN to identify tRNA genes."}