PMC:4502367 / 13149-14130 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502367","sourcedb":"PMC","sourceid":"4502367","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502367","text":"The trained GeneMark.hmm (Lukashin and Borodovsky 1998) and Augustus programs were used to predict gene models. For Z. tritici, Fgenesh (Salamov and Solovyev 2000) gene models obtained from the first annotation by JGI (Goodwin et al. 2011) were also included. Gene models obtained from the trained gene predictors were evaluated and combined using the EVidenceModeler (EVM) software (Haas et al. 2008) to create a weighted consensus of the gene structures. Weights of 3, 5, and 7 were used for ab initio predictions, homology-based predictions, and transcript evidence, respectively. Homology-based gene models obtained from GeneWise (Birney et al. 2004) were only used for Z. tritici as reliable gene models; they could not be obtained in the much more fragmented genomes of Z. pseudotritici, Z. ardabiliae, and Z. brevis. Based on transcript alignments, the PASA pipeline was used to correct the consensus gene model structure and to resolve conflicts between different isoforms.","tracks":[{"project":"2_test","denotations":[{"id":"25917918-9461475-43386549","span":{"begin":50,"end":54},"obj":"9461475"},{"id":"25917918-10779491-43386550","span":{"begin":158,"end":162},"obj":"10779491"},{"id":"25917918-21695235-43386551","span":{"begin":234,"end":238},"obj":"21695235"},{"id":"25917918-18190707-43386552","span":{"begin":396,"end":400},"obj":"18190707"},{"id":"25917918-15123596-43386553","span":{"begin":649,"end":653},"obj":"15123596"}],"attributes":[{"subj":"25917918-9461475-43386549","pred":"source","obj":"2_test"},{"subj":"25917918-10779491-43386550","pred":"source","obj":"2_test"},{"subj":"25917918-21695235-43386551","pred":"source","obj":"2_test"},{"subj":"25917918-18190707-43386552","pred":"source","obj":"2_test"},{"subj":"25917918-15123596-43386553","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ec9a","default":true}]}]}}