The final assembly can be downloaded in the complete GFF file, with complete annotation of the features (Proteins and tRNA). The chromosome name corresponds to the homologous chromosome of the reference Saccharomyces cerevisiae.
Protein and cDNA fasta files contain exonerate and de novo gene predictions. Feature names are as follows:
- Syntenic genes have the same name as the Saccharomyces cerevisiae ortholog regardless of chromosomal number or position.
- Non-syntenic genes with similar sequence as Saccharomyces cerevisiae have the same name as their most similar sequence Saccharomyces cerevisiae homolog.
- Novel genes have an arbitrary name given by Genemark that corresponds to the ORF number.
- Syntenic tRNA which code for the same codon as Saccharomyces cerevisiae are named after the Saccharomyces cerevisiae tRNA name.
- Non-syntenic tRNA or tRNAs that code for a different codon than the reference were given a new name.
DNA sequences can be blasted to the final assembly of Saccharomyces arboricolus (blastn) and protein sequences can be blasted against the predicted protein sequences (blastp).
Output can be a linked table or the raw blast output. The linked table allows the user to click on a row and obtain the blast hit sequence or to view the blast hit within the genome browsers.
The genome browser displays the synteny of Saccharomyces arboricolus genes against Saccharomyces cerevisiae and Saccharomyces bayanus. Clicking on a gene will bring the DNA sequence coding for the feature as well as protein translations. On that details page, clicking on the chromosomal coordinates will bring the species-specific genome browser, which allows more sophisticated data queries (such as selecting an area and extracting its sequence).
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