maize-GAMER Annotations for maize B73 RefGen_V4 Zm00001d.2 /_readme.txt - this file * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Please note, 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 such as 7-Zip (free and open source * * available from http://www.7-zip.org)to open and decompress the archive. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * maize B73 RefGen_v3 data can be found at DOI: https://doi.org/10.7946/P2S62P * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Final clean annotation file is found in the e.agg_data directory. * * maize.B73.AGPv4.aggregate.gaf.gz file is the final product of the * * pipeline. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * /a._mm_gaf: This directory contains 4 files File Name | Description ------------------------------------------+------------------------------------- 1 _mm_gaf-desc.txt | Detailed description of the contents | of data files in a._mm_gaf folder | 2. maize.B73.AGPv4.argot2.5.gaf.gz | The raw output from Argot2.5 | converted into GAF format | 3. maize.B73.AGPv4.fanngo.gaf.gz | The raw output from FANN-GO | converted into GAF format | 4. maize.B73.AGPv4.pannzer.gaf.gz | The raw output from PANNZER | converted into GAF format /b._raw_gaf: This directory contains 7 files File Name | Description ------------------------------------------+------------------------------------- 1 _raw_gaf-desc.txt | Detailed description of the contents | of data files in b._raw_gaf folder | 2. maize.B73.AGPv4.argot2.5.gaf.gz | A subset of GO annotations selected | from maize.B73.AGPv4.argot2.5.gaf.gz | after removing low confidence | annotations based on annotation | scores | 3. maize.B73.AGPv4.fanngo.gaf.gz | A subset of GO annotations selected | from maize.B73.AGPv4.fanngo.gaf.gz | after removing low confidence | annotations based on annotation | scores | 4. maize.B73.AGPv4.Interproscan5.gaf.gz | Output from InterProScan pipeline | for maize AGPv3 covereted into GAF | 2.0 format | 5. maize.B73.AGPv4.pannzer.gaf.gz | A subset of GO annotations selected | from maize.B73.AGPv4.pannzer.gaf.gz | after removing low confidence | annotations based on annotation | scores | 6. maize.B73.AGPv4.arabidopsis.gaf.gz | GO annotations in GAF format for | maize from sequence similarity | method used with TAIR datasets | 7. maize.B73.AGPv4.uniprot.plants.gaf.gz | GO annotations in GAF format for | maize from sequence similarity | method used with UniProt datasets /c._uniq_gaf - This directory contains 7 files File Name | Description ------------------------------------------+------------------------------------- 1 _uniq_gaf_desc.txt | Detailed description of the contents | of data files in c.uniq_gaf folder | 2. maize.B73.AGPv4.argot2.5.gaf.gz | Non-duplicate annotations from | Argot2.5 maize GO dataset | 3. maize.B73.AGPv4.fanngo.gaf.gz | Non-duplicate annotations from | FANN-GO maize GO dataset | 4. maize.B73.AGPv4.Interproscan5.gaf.gz | Non-duplicate annotations from | InterProScan maize GO dataset | 5. maize.B73.AGPv4.pannzer.gaf.gz | Non-duplicate annotations from | PANNZER maize GO dataset | 6. maize.B73.AGPv4.arabidopsis.gaf.gz | Non-duplicate annotations for maize | from TAIR-sequence-similarity | GO dataset | 7. maize.B73.AGPv4.uniprot.plants.gaf.gz | Non-duplicate annotations for | maize from UniProt-sequence- | similarity GO dataset /d._non_red_gaf - This directory contains 7 files File Name | Description ------------------------------------------+------------------------------------- 1 _non_red_gaf_desc.txt | Detailed description of the contents | of data files in d._non_red_gaf | folder | 2. maize.B73.AGPv4.argot2.5.gaf.gz | Non-duplicate and non-redundant | annnotations from Argot2.5 maize | GO dataset produced by maize-GAMER | 3. maize.B73.AGPv4.fanngo.gaf.gz | Non-duplicate and non-redundant | annnotations from FANN-GO maize | GO dataset produced by maize-GAMER | 4. maize.B73.AGPv4.Interproscan5.gaf.gz | Non-duplicate and Non-redundant | InterProScan annotations maize | produced by maize-GAMER | 5. maize.B73.AGPv4.pannzer.gaf.gz | Non-duplicate and non-redundant | annnotations from PANNZER maize | GO dataset produced by maize-GAMER | 6. maize.B73.AGPv4.arabidopsis.gaf.gz | Non-duplicate and Non-redundant | maize GO annotations from sequence | similarity method using with TAIR | dataset prouced for maize-GAMER | 7. maize.B73.AGPv4.uniprot.plants.gaf.gz | Non-duplicate and Non-redundant | maize GO annotations from sequence | similarity method using with | UniProt dataset produced for | maize-GAMER /e.agg_data - This directory contains 2 files File Name | Description ------------------------------------------+------------------------------------- 1 _agg_data_description.txt | Detailed description of the contents | of data files in e.agg_data folder | 2. maize.B73.AGPv4.aggregate.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/