CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.

ABSTRACT:

Motivation

The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.

Results

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 f

SUBMITTER: Pedersen BS 

PROVIDER: S-EPMC3834799 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature