maize-GAMER /_readme.txt - this file * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Please note, most of the data files contained in this DOI are * * compressed into GZip files (.gz extension). * * Mac and Linux OS's can extract this file type natively. * * Windows OS requires software to extract the archive. 7-Zip * * (http://www.7-zip.org) is free and open source software that will * * allow windows PCs to open and decompress the archive. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Final clean annotation file is found in the e.agg_data directory. * * maize_v3.agg.nr.gaf.gz file is the final product of the pipeline. * * maize_v3.gramene49.gaf.gz & maize_v3.phytozome.gaf.gz in the * * d.non_red_gaf might also be of interest for clean public maize datasets * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * /a._mm_gaf: This directory contains 3 files File Name | Description ------------------------------+----------------------------------------------- 1 _mm_gaf-desc.txt | Detailed description of the contents of data | files in this directory | 2. argot2-0.0.gaf.gz | The raw output from Argot2 converted into | GAF format | 3. fanngo-0.0.gaf.gz | The raw output from FANN-GO converted into | GAF format | 4. pannzer-0.0.gaf.gz | The raw output from PANNZER converted into | GAF format /b._raw_gaf: This directory contains 11 files File Name | Description ------------------------------+----------------------------------------------- 1 _raw_gaf-desc.txt | Detailed description of the contents of data | files in this directory | 2. maize_v3.agrigo.gaf.gz | GO annotations for maize downloaded from | agrigo website and coverted into GAF 2.0 | format | 3. maize_v3.argot2.gaf.gz | A subset of GO annotations selected from | a.mm_gaf/argot2-0.0.gaf.gz after removing low | confidence annotations based on annotation | scores | 4. maize_v3.fanngo.gaf.gz | A subset of GO annotations selected from | a.mm_gaf/fanngo-0.0.gaf.gz after removing low | confidence annotations based on annotation | scores | 5. maize_v3.gold.gaf.gz | Gold standard GO annotations for maize B73 | AGPv3 provided by MaizeGDB | 6. maize_v3.gramene49.gaf.gz | GO annotations downloaded from Gramene | database for maize B73 AGPv3 | 7. maize_v3.iprs.gaf.gz | Output from InterProScan pipeline for maize | AGPv3 covereted into GAF 2.0 format | 8. maize_v3.pannzer.gaf.gz | A subset of GO annotations selected from | a.mm_gaf/pannzer-0.0.gaf.gz after removing low | confidence annotations based on annotation | scores | 9. maize_v3.phytozome.gaf.gz | GO annotations for maize downloaded from | Phytozome website and coverted into GAF 2.0 | format | 10. maize_v3.tair.hc.gaf.gz | GO annotations in GAF format for maize from | sequence similarity method used with TAIR | datasets | 11. maize_v3.uniprot.gaf.gz | GO annotations in GAF format for maize from | sequence similarity method used with UniProt | datasets /c._uniq_gaf - This directory contains 11 files File Name | Description ------------------------------+----------------------------------------------- 1 _uniq_gaf_desc.txt | Detailed description of the contents of data | files in this directory | 2. maize_v3.agrigo.gaf.gz | Non-duplicate annotations from AgriGO maize | GO dataset | 3. maize_v3.argot2.gaf.gz | Non-duplicate annotations from Argot2 maize | GO dataset | 4. maize_v3.fanngo.gaf.gz | Non-duplicate annotations from FANN-GO maize | GO dataset | 5. maize_v3.gold.gaf.gz | Non-duplicate gold standard GO annotations for | maize | 6. maize_v3.gramene49.gaf.gz | Non-duplicate Gramene GO annotations for maize | 7. maize_v3.iprs.gaf.gz | Non-duplicate annotations from InterProScan | maize GO dataset | 8. maize_v3.pannzer.gaf.gz | Non-duplicate annotations from PANNZER maize | GO dataset | 9. maize_v3.phytozome.gaf.gz | Non-duplicate annotations from Phytozome maize | GO dataset | 10. maize_v3.tair.hc.gaf.gz | Non-duplicate annotations for maize from TAIR- | sequence-similarity GO dataset | 11. maize_v3.uniprot.gaf.gz | Non-duplicate annotations for maize from | UniProt-sequence-similarity GO dataset /d._non_red_gaf - This directory contains 11 files File Name | Description ------------------------------+----------------------------------------------- 1 _non_red_gaf_desc.txt | Detailed description of the contents of data | files in this directory | 2. maize_v3.agrigo.gaf.gz | Non-duplicate and non-redundant annotations | from the AgriGO dataset | 3. maize_v3.argot2.gaf.gz | Non-duplicate and non-redundant annnotations | from Argot2 maize GO dataset produced by | maize-GAMER | 4. maize_v3.fanngo.gaf.gz | Non-duplicate and non-redundant annnotations | from FANN-GO maize GO dataset produced by | maize-GAMER | 5. maize_v3.gold.gaf.gz | Non-duplicate and Non-redundant Gold standard | GO annotations for maize | 6. maize_v3.gramene49.gaf.gz | Non-duplicate and Non-redundant Gramene maize | GO dataset | 7. maize_v3.iprs.gaf.gz | Non-duplicate and Non-redundant InterProScan | annotations maize produced by maize-GAMER | 8. maize_v3.pannzer.gaf.gz | Non-duplicate and non-redundant annnotations | from FANN-GO maize GO dataset produced by | maize-GAMER | 9. maize_v3.phytozome.gaf.gz | Non-duplicate and Non-redundant Phytozome | maize GO dataset | 10. maize_v3.tair.hc.gaf.gz | Non-duplicate and Non-redundant maize GO | annotations from sequence similarity method | using with TAIR datasets prouced for | maize-GAMER | 11. maize_v3.uniprot.gaf.gz | Non-duplicate and Non-redundant maize GO | annotations from sequence similarity method | using with UniProt datasets prouced for | maize-GAMER /e._agg_data - This directory contains 3 files File Name | Description ------------------------------+----------------------------------------------- 1 _agg_data_description.txt | Detailed description of the contents of data | files in this directory | 2. maize_v3.agg.gaf.gz | The aggregate dataset produced by maize-GAMER | with duplication and redundancy | 3. maize_v3.agg.nr.gaf.gz | The clean aggregate dataset produced by | maize-GAMER without duplication and redundancy * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * For questions regarding released datasets contact: Corresponding Author: Carolyn Lawrence-Dill (Iowa State University) triffid@iastate.edu https://dill-picl.org/projects/maize-gamer