Annotate: Annotation of single-nucleotide variants in the yeast genome

Annotate is a software package that annotates mutations in a genome sequence for possible functional consequences. The software takes a BED file containing the location and identity of mutations, a parental genome sequence, and an annotations file as input, and outputs the annotation for each mutation. If mutations occur in coding sequences, the software will determine the possible changes to protein sequence. Annotate is written in Python. To cite Annotate, please use the following publications:

The Yeast Alix Homolog Bro1 Functions as a Ubiquitin Receptor for Protein Sorting into Multivesicular Endosomes. Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. Dev Cell. 2013 Jun; 25(5):520-533.

Data Files

Mutations to be annotated should be provided in a simple BED file containing the chromosome, start position, stop position, parental allele, and derived allele. For example:

chr1   213941196  213941196  A  G
chr10  942363     942363     C  G	

Annotate currently relies on three data files to perform annotations - a FASTA file of the parental genome sequence, a FASTA file of coding sequences, and a GFF file containing annotations. These files are included in the Annotate-0.1.tar.gz download, but the most up-to-date versions can be downloaded at the Saccharomyces Genome Database.


Read the documentation


For support of Annotate, please write to Matt Rich (mattrich at uw dot edu)

Source code

Current version (0.1)