biostudies-literaturePedersen BSNCI NIH HHS3003-6https://www.ebi.ac.uk/biostudies/studies/S-EPMC3834799biostudies-literatureUnknown29(23)<h4>Motivation</h4>The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.<h4>Results</h4>We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions-exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant fBioinformatics (Oxford, England)CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.PMC3834799P50 CA058187U54CA143798Yang IVDe SPedersen BSfalseCruzDB: software for annotation of genomic intervals with UCSC genome-browser database.<h4>Motivation</h4>The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.<h4>Results</h4>We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions-exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant f2013-01-01T00:00:00Z2013 Dec2025-04-04T12:26:47.591Z2019-03-27T03:08:58ZS-EPMC38347992403721210.1093/bioinformatics/btt534