nre.cb.bscb.cornell.edu

NRE

Neutrally evolving regions are essential for understanding human demographic history, for the design of sequencing experiments, and in other studies calling for data impervious to the confounding effects of natural selection. However, extracting such regions from the genome can be an elaborate, laborious, imprecise feat without the proper tool. This is the home of Neutral Region Explorer. NRE currently runs on human assembly hg19. And 1000 genomes consortium phase I. Please visit the VERSIONS.

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NRE | nre.cb.bscb.cornell.edu Reviews

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Neutrally evolving regions are essential for understanding human demographic history, for the design of sequencing experiments, and in other studies calling for data impervious to the confounding effects of natural selection. However, extracting such regions from the genome can be an elaborate, laborious, imprecise feat without the proper tool. This is the home of Neutral Region Explorer. NRE currently runs on human assembly hg19. And 1000 genomes consortium phase I. Please visit the VERSIONS.

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NRE | nre.cb.bscb.cornell.edu Reviews

https://nre.cb.bscb.cornell.edu

Neutrally evolving regions are essential for understanding human demographic history, for the design of sequencing experiments, and in other studies calling for data impervious to the confounding effects of natural selection. However, extracting such regions from the genome can be an elaborate, laborious, imprecise feat without the proper tool. This is the home of Neutral Region Explorer. NRE currently runs on human assembly hg19. And 1000 genomes consortium phase I. Please visit the VERSIONS.

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nre.cb.bscb.cornell.edu

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NRE: Run

http://nre.cb.bscb.cornell.edu/nre/run.html

Select Regions to Exclude. Upload Additional Regions to Exclude. Minimum region size (bp). Eg 200, leave blank to omit filter). Distance to nearest gene. Eg min 0.1 cM, leave blank to omit filter). Uses RefSeq transcripts as genes, or . Upload your own definition of regions. From which to measure distance. Eg min 0.7, leave blank to omit filter). Min BG selection coefficient. Eg 095, leave blank to omit filter). Eg 1-5,7,X). Select Regions for which to Calculate % Overlap. Repeat Masker v3.27.

2

NRE: Guide

http://nre.cb.bscb.cornell.edu/nre/tut.html

Mechanism for the easy extraction and analysis of neutral regions from the human genome. In the first step, annotated loci and/or user-provided loci are combined. Results by one or more chosen criterion, separately or simultaneously, to refine the data set. Results can be previewed, downloaded in standard formats, or exported to the 1000 Genomes or UCSC genome browsers. Please see below for guides to each section. Inlcuding descriptions of methods. Quick links to each section:. Genomic regions to exclude.

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NRE: Frequently Asked Questions

http://nre.cb.bscb.cornell.edu/nre/faq.html

What kind of output does NRE produce? How long should my query take? What are all the columns/filtering parameters? Where do the estimates for diversity, recombination rate, and distance to the nearest gene come from? What is the difference between genomic regions to exclude and genomic regions for which to calculate percent overlap? Why is my output blank? Where can I download the available filter tracks, or additional tracks to use as filters? I have other questions/comments/suggestions. And other publ...

4

NRE: Worked Example

http://nre.cb.bscb.cornell.edu/nre/example.html

This page provides a worked example. To get you started with the use of NRE. While a detailed and recommended explanation of all options is offered in the Guide. Link at top of page), here we will work through an example to produce a stringent set of candidate neutral regions. And explore some of NRE's additional features. The first step can be reached by clicking on the blue. Link at the top of the page. Can be reached by clicking the help link (? At the top right corner of each section. Either because ...

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NRE

http://nre.cb.bscb.cornell.edu/nre/index.html

Neutrally evolving regions are essential for understanding human demographic history, for the design of sequencing experiments, and in other studies calling for data impervious to the confounding effects of natural selection. However, extracting such regions from the genome can be an elaborate, laborious, imprecise feat without the proper tool. This is the home of Neutral Region Explorer. NRE currently runs on human assembly hg19. And 1000 genomes consortium phase I. Please visit the VERSIONS.

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Tools & Data | Keinan Lab

http://keinanlab.cb.bscb.cornell.edu/content/tools-data

Recent and Selected Publications. Alon Keinan's NCBI MyBibliography (pubmed). Two new postdoctoral positions available in the lab. Release of a much improved X chromosome analysis toolsest (XWAS v1.1). Our paper on selection of a vegetarian allele piqued the interest of many in the media. Alon Keinan to teach Coalescent Theory and Human Population Genomics. Upcoming presentations at ASHG 2015. New software: EGGS efficiently estimates sfs for generalized-growth demography models. 13, 301 (2012). A Keinan,...

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nre.cb.bscb.cornell.edu

NRE

Neutrally evolving regions are essential for understanding human demographic history, for the design of sequencing experiments, and in other studies calling for data impervious to the confounding effects of natural selection. However, extracting such regions from the genome can be an elaborate, laborious, imprecise feat without the proper tool. This is the home of Neutral Region Explorer. NRE currently runs on human assembly hg19. And 1000 genomes consortium phase I. Please visit the VERSIONS.

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