title: UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.
abstract: When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to ten builds of the Ensembl human genome spanning eight years to demonstrate this stability. The implementation of UniqTag in Ruby and an R package are available at https://github.com/sjackman/uniqtag sjackman/uniqtag. The R package is also available from CRAN: install.packages ("uniqtag"). Supplementary material and code to reproduce it is available at https://github.com/sjackman/uniqtag-paper.
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: İnanç
authors.initials: İ
authors.lastname: Birol
mesh_terms: D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software