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.

Version 2
Much faster, more rigorous, than Version 1

GERP 2 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.

GERP 2.1 beta (written by Eugene Davydov, Batzoglou lab) is the current version of GERP. The C source code and a test data set are available for download off the links on the right.

New in v2.1:

Lots of under-the-hood changes for gerpelem resulting in better memory management and more robust false-positive rate calculations.

Shuffled alignments now exclude the most constrained fraction of elements; this facilitates comparable sensitivity between alignments that are constraint-dense, and alignments that are constraint-poor.

No changes for gerpcol.

GERP Downloads

GERP 2.1b
(zipped tar, Feb 11 2008)

GERP test data
(zipped tar, Feb 11 2008)

Original GERP Paper (pdf)

Supplemental Materials Page