PipHelper retrieves sequence as well as annotation data from the UCSC Genome Browser and generates sequence, repeats, and exons files suitable for further processing by PipMaker and MultiPipMaker.

Repeats in the returned sequence have been "soft masked" using RepeatMasker as described in the UCSC Data and Downloads FAQ.

The application itself can be found here:


To use PipHelper, you need to choose an assembly, enter a position, and optionally choose an annotation.

A screenshot of the PipHelper selection screen:

PipHelper selection screenshot


PipHelper generates text files which can be downloaded to your computer, and submitted to PipMaker and MultiPipMaker.

Sample output for hg17, chr11:100000-200000, RefSeq Genes

A screenshot of the PipHelper output screen:

PipHelper output screenshot