PMC:4502367 / 18693-20310
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502367","sourcedb":"PMC","sourceid":"4502367","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502367","text":"RNA-seq data and detailed homology searches allowed us to generate an improved annotation of gene models in the IPO323 Z. tritici reference genome. Read data obtained from in planta and in vitro experiments were filtered (Table S1) and used for transcriptome assembly. Assemblies were based on two different but complementary approaches: (i) de novo, where the reads were assembled without a reference sequence and (ii) genome-guided, where the IPO323 reference genome was used as a template for transcript assemblies. In total, 68,653 transcripts were generated by the de novo method and 73,127 transcripts by the genome-guided method (Table 1). These transcripts were used to create a final database containing 13,847 putative gene models next used for the generation of a training set for ab initio predictors and for the correction of predicted gene models. We generated a final training set of 1611 gene models that was used to train two ab initio gene predictors: Augustus (Stanke and Waack 2003) and GeneMark-hmm (Lukashin and Borodovsky 1998). The outputs of these software were combined with 10,893 predicted gene models of another ab initio predictor, Fgenesh (Salamov and Solovyev 2000), obtained from the JGI annotation. We thereby obtained a total of 36,423 different gene models combining models from Augustus, GeneMark-hmm, and Fgenesh. These gene models were processed by EVidence Modeler (EVM) (Haas et al. 2008) to identify a consensus model for each gene. Finally, corrections were applied to the gene models using PASA (Haas et al. 2003) and the previously reconstructed RNA-seq-based transcripts.","tracks":[{"project":"2_test","denotations":[{"id":"25917918-14534192-43386568","span":{"begin":997,"end":1001},"obj":"14534192"},{"id":"25917918-9461475-43386569","span":{"begin":1045,"end":1049},"obj":"9461475"},{"id":"25917918-10779491-43386570","span":{"begin":1192,"end":1196},"obj":"10779491"},{"id":"25917918-18190707-43386571","span":{"begin":1424,"end":1428},"obj":"18190707"},{"id":"25917918-14500829-43386572","span":{"begin":1552,"end":1556},"obj":"14500829"}],"attributes":[{"subj":"25917918-14534192-43386568","pred":"source","obj":"2_test"},{"subj":"25917918-9461475-43386569","pred":"source","obj":"2_test"},{"subj":"25917918-10779491-43386570","pred":"source","obj":"2_test"},{"subj":"25917918-18190707-43386571","pred":"source","obj":"2_test"},{"subj":"25917918-14500829-43386572","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#a0ec93","default":true}]}]}}