Maize B104 (beta) genome assembly and annotation
Bibliographic record
Abstract
In the interest of the maize research community, the Iowa State Transformation Facility and Lawrence-Dill Plant Informatics and Computation Lab in collaboration with MaizeGDB has released a beta-version of the B104 maize genome and structural annotations prior to scientific publication in accordance with guidelines set forth by the Toronto agreement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html) for prepublication data sharing (Nature. 2009 461:168). The above groups reserve the first right to publish on the available B104 data including but not limited to whole-genome comparisons, genes, structural annotations, functional annotations, and genome-wide association studies. The group also reserves the right to the first opportunity to improve this sequence and its annotations for a full official genome release (version 1; anticipated release December 2017). Under the Toronto agreement, researchers can use the B104 sequence and annotation to study individual or small sets of genes and localized regions of the genome. Any redistribution of these data should include the full text of the data use policy.<br><br><br>Assembly Note: <br>The B104 genome was sequenced using Illumina paired end sequencing on HiSeq2000 at raw read coverage of 50X with read length of 101 bp and insert size 250 bp. Trimmed reads were assembled using a reference- guided assembly approach with B73 reference sequence (AGPv2 5b pseudo molecules). The reads were mapped to the B73 reference, consensus sequences were generated and gaps were filled. All paired end reads were mapped back to the gap-filled scaffolds to identify the regions with abnormal links and corresponding scaffolds were broken from those regions. Unmapped reads were assembled using a de novo approach and scaffolds were added to the final assembly.<br><br>B104 Gene Models:<br><br>B104 (beta) gene models were developed by the Lawrence-Dill Plant Informatics Lab in collaboration with MaizeGDB and Dow AgroSciences, and made available through www.maizegdb.org.<br><br>Genes were annotated using MAKER-P Pipeline, using both evidence-based approach (cDNA and EST data) and an ab initio approach. For evidence based prediction, transcriptome assemblies of diverse tissue types from B104 and other maize lines (B73, Miami white, Mo17, OH43, B97, W22, A188), full length cDNA sequences and annotated B73 proteins from NCBI, Arabidopsis thaliana, Oryza sativa japonica and other plant proteins from Uniprot were used. For ab initio predictions, AUGUSTUS and SNAP gene predictors were used. Gene models are named as recommended by the Maize Nomenclature Committee. <br>
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.144 | 0.269 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".