Table 7.
Programming recipes to analyze data in Ensembl Plants, including perl API (A), R BiomaRt (B), FTP (F), SQL (S), REST (R), and Ensembl VEP (V) examples. These recipes and their software dependencies, together with a few more scripts for phylogenomic analyses, are updated at https://github.com/Ensembl/plant-scripts
| Recipe | Description |
|---|---|
| A1 | Load the Registry object with details of genomes available |
| A2 | Check which analyses are available for a species |
| A3 | Get soft-masked sequences from Arabidopsis thaliana |
| A4 | Get BED file with repeats in chr4 |
| A5 | Find the DEAR3 gene |
| A6 | Get the transcript used in Compara analyses |
| A7 | Find all orthologues of a gene |
| A8 | Get markers mapped on chr1D of bread wheat |
| A9 | Find all syntelogues among rices |
| A10 | Print all translations for other features genes |
| B1 | Check plant marts and select dataset |
| B2 | Check available filters and attributes |
| B3 | Download GO terms associated with genes |
| B4 | Get Pfam domains annotated in genes |
| B5 | Get SNP consequences from a selected variation source |
| C1 | Find RNA-seq CRAM files for a genome assembly |
| F1 | Download peptide sequences in FASTA format |
| F2 | Download CDS nucleotide sequences in FASTA format |
| F3 | Download transcripts (cDNA) |
| F4 | Download soft-masked genomic sequences |
| F5 | Upstream/downstream sequences |
| F6 | Get mappings to UniProt proteins |
| F7 | Get indexed, bgzipped VCF file with variants mapped |
| F8 | Get precomputed VEP cache files |
| F9 | Download all homologies in a single TSV file, several GBs |
| F10 | Download UniProt report of Ensembl Plants |
| F11 | Retrieve list of new species in current release |
| F12 | Get current plant species tree cladogram |
| S1 | Check currently supported Ensembl Genomes (EG) core schemas |
| S2 | Count protein-coding genes of a particular species |
| S3 | Get stable_ids of transcripts used in Compara analyses |
| S4 | Get variants significantly associated to phenotypes |
| S5 | Get Triticumaestivumhomeologous genes across A, B, and D subgenomes |
| S6 | Count the number of whole-genome alignments of all genomes |
| S7 | Extract all the mutations and consequence for a known line on triticum_aestivum |
| R1 | Create an HTTP client and helper functions |
| R2 | Get metadata for all plant species |
| R3 | Find features overlapping genomic region |
| R4 | Fetch phenotypes overlapping genomic region |
| R5 | Find homologues of selected gene |
| R6 | Get annotation of orthologous genes/proteins |
| R7 | Fetch variant consequences for multiple variant ids |
| R8 | Check consequences of single SNP within CDS sequence |
| R9 | Retrieve variation sources of a species |
| V1 | Download, install, and update VEP |
| V2 | Unpack downloaded cache file and check SIFT support |
| V3 | Predict effect of variants |
| V4 | Predict effect of variants for species not in Ensembl |