GERP protocols

GERP specifications

Information


Unique identifier OMICS_00174
Name GERP
Alternative names Genomic Evolutionary Rate Profiling, GERP++, GERP2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://mendel.stanford.edu/SidowLab/downloads/gerp/gerp++.tar.gz
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


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Maintainer


  • person_outline Arend Sidow <>

Publications for Genomic Evolutionary Rate Profiling

GERP IN pipelines

 (21)
2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] \begin{document}$\hat {f_{d}}$\end{document}fd^ distribution in the south american lowland population as the cutoff., we estimated the individual burden of deleterious alleles based on gerp scores [89] for each site in the maize genome, which reflects the strength of purifying selection based on constraint in a whole genome alignment of 13 plant species [90]. the alignment […]

2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] [89] for each site in the maize genome, which reflects the strength of purifying selection based on constraint in a whole genome alignment of 13 plant species [90]. the alignment and estimated gerp scores are available at iplant (https://doi.org/10.7946/p2ws60). scores above 0 may be interpreted as historically subject to purifying selection, and mutations at such sites are likely […]

2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] as ancestral and defined the non-sorghum allele as the deleterious allele. only biallelic sites were included for our evaluation. inclusion of the maize b73 reference genome when calculating gerp scores [90] introduces a bias toward underestimation of the burden of deleterious alleles in maize versus teosinte populations. therefore, we corrected the gerp scores of sites where the b73 […]

2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] b73 reference genome when calculating gerp scores [90] introduces a bias toward underestimation of the burden of deleterious alleles in maize versus teosinte populations. therefore, we corrected the gerp scores of sites where the b73 allele is derived following [7]. briefly, we divided snps where the b73 allele is ancestral into bins of 1% derived allele frequency based on maize hapmap3 [91] […]

2017
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] we divided snps where the b73 allele is ancestral into bins of 1% derived allele frequency based on maize hapmap3 [91] and used this frequency distribution to estimate the posterior probability of gerp scores for snps where the b73 allele is derived., the sum of gerp scores multiplied by deleterious allele frequency for each snp site was used as a proxy of individual burden of deleterious […]

GERP institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Biomedical Informatics Program, Stanford University, Stanford, CA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
GERP funding source(s)
Supported in part by an Encode subcontract (PI, Richard Myers), NIH/NHGRI, US National Library of Medicine (K22 LM008261 and T15 LM007033), andin part by NSF grant #0347952.

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