MOTIVATION: In the evolution of species, a kind of special sequences, termed 
ultraconserved sequences (UCSs), have been inherited without any change, which 
strongly suggests those sequences should be crucial for the species to survive 
or adapt to the environment. However, the UCSs are still regarded as mysterious 
genetic sequences so far. Here, we present a systematic study of ultraconserved 
genomic regions in the budding yeast based on the publicly available genome 
sequences, in order to reveal their relationship with the adaptability or 
fitness advantages of the budding yeast.
RESULTS: Our results indicate that, in addition to some fundamental biological 
functions, the UCSs play an important role in the adaptation of Saccharomyces 
cerevisiae to the acidic environment, which is backed up by the previous 
observation. Besides that, we also find the highly unchanged genes are enriched 
in some other pathways, such as the nutrient-sensitive signaling pathway. To 
facilitate the investigation of unique UCSs, the UCSC Genome Browser was 
utilized to visualize the chromosomal position and related annotations of UCSs 
in S.cerevisiae genome.
AVAILABILITY AND IMPLEMENTATION: For more details on UCSs, please refer to the 
Supplementary information online, and the custom code is available on request.
CONTACT: fgao@tju.edu.cn.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.