Stanford University logo
Path Dept logo
Genetics Dept logo
SOM logo


Genomic Evolutionary Rate Profiling: GERP

GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions". Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element.

GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using 'shuffled' alignments in which the order of columns is randomized.

GERP++ Programs

GERP++ (previously referred to as GERP2) consists of two programs, gerpcol and gerpelem. Gerpcol esimates constraint for each column of the alignment; gerpelem then identifies constrained elements from gerpcol's output.

Download software and papers from the links on the right.

GERP Elements and Base-Specific Calls

We have precomputed elements and base-wise RS scores for human and mouse genomes, assemblies hg18, hg19, and mm9, using the mammalian alignments available at UCSC in late 2010. Please see the links on the right. Caution: big files.



GERP++ Code

GERP++ code
(zipped tar, May 22 2011)

GERP test data
(zipped tar, Feb 11 2008)

GERP Papers

GERP++ paper (pdf)

Original GERP Paper (pdf)

Supplemental Materials Page

GERP++ Tracks Data

hg 19, base-wise scores (6.3 GB!)
hg 19, elements (18 MB)

hg 18, base-wise scores (6.3 GB!)
hg 18, elements (28 MB)

mm9, base-wise scores (2.6 GB!)
mm9, elements (14 MB)

Readme on the tracks