期刊
GENOME RESEARCH
卷 15, 期 8, 页码 1051-1060出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.3642605
关键词
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资金
- NHGRI NIH HHS [F32 HG002325, HG02238, HG02325, R01 HG002238] Funding Source: Medline
- NIDDK NIH HHS [R56 DK065806, DK65806, R01 DK065806] Funding Source: Medline
Techniques of comparative genomes are being used to identify candidate functional DNA sequences, and objective evaluations are needed to assess their effectiveness. Different analytical methods score distinctive features of whole-genome alignments among human, Mouse, and rat to predict functional regions. We evaluated three of these methods for their ability to identify the positions of known regulatory regions in the well-studied HBB gene complex. Two methods, multispecies conserved sequences and phastCons, quantify levels of conservation to estimate a likelihood that aligned DNA sequences are under purifying selection. A third function, regulatory potential (RP), measures the similarity of patterns in the alignments to those in known regulatory regions. the methods call correctly identify 50%-60% of noncoding positions in the HBB gene complex as regulatory or nonregulatory, with RP performing better than do other methods. When evaluated by the ability to discriminate genomic intervals, RP reaches a sensitivity of 0.78 and a true discovery rate of similar to 0.6. the performance is better oil other reference sets; both phastCons and RP scores call capture almost all regulatory elements in those sets along with similar to 7% of the human genome.
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