Create a text info file based on a Genome object.
This intended purpose of this App is to produce a downloadable TEXT file about an object.
Most KBase data objects already have some type of viewable HTML table, either as output from an App or by dragging the object onto the Narrative. This App serves a different purpose. It creates data files that are downloadable and used with local tools such as Excel or informatic scripts.
This App creates files on a Genome. A Summary section has a preview of the full output. It is intended to be a preview of the downloadable file. If the file is tab or comma delimited, it may appear misaligned on the screen but readable by a computer script. The HTML link opens a new tab with the full output. The link for downloading the files is in the Files section of the output.
- The KBase Genome object.
- A download option:
- Protein coding Features, Tab-delimited and comma-delimited. A file where the rows are the genes in the Genome and the columns are information about the genes. Columns are separated with tabs or commas.
- Features in GFF3 format. A GFF3 (General Feature Format) file of the protein coding features in the Genome.
- FASTA, translated CDSs. A FASTA-formatted file of the amino acid sequences of the protein coding features.
- FASTA, of mRNAs. A FASTA-formatted file of the mRNA sequences of the protein coding features.
- DNA FASTA format. Create a FASTA file of the genomic DNA.
- The Summary or Link section has text version of the requested file.
- One downloadable file in the Files section for each output selection. The name and content of the file will depend on the requested file format.
- FASTA files will be in FASTA format. The file name will end in .fna for nucleotide files and .faa for amino acid files.
- Feature lists will include the FeatureID, Feature Type, Contig, Location (Feature Coordinates), Strand, Feature Function, and, if applicable, Aliases. Tab-delimited, comma-delimited, and GFF files will end in .tab, .csv and .gff, respectively.
- Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163 , https://www.nature.com/articles/nbt.4163
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