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Online Nucleosomes Position Prediction by Genomic Sequence

This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers: * Segal et al., A Genomic Code for Nucleosome Positioning, Nature 2006 * Field et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Comp Biol. 2008 * Kaplan et al., The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Nature 2008 We recommend using the latest version of the model (Version 3), which is applicable to all species. Paste in a sequence to analyze or upload file. You can provide multiple sequences in fasta format (separate sequences by lines starting with '>' followed by the sequence name). The length of each sequence must be between 147bp and 40kb bp. Note: Due to boundary effects, we highly recommend that you add at least 5000 bp of flanking sequence around your sequence of interest. You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts.

URL: http://genie.weizmann.ac.il/software/nucleo_prediction.html

Resource ID: nlx_23258     Resource Type: Resource     Version: Latest Version

Synonyms

Nucleosomes Position Prediction

Additional Resource Types

data analysis service, software resource

Supercategory

Resource

Parent Organization

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am June 1, 2011

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 4 years ago by Anonymous

A genomic code for nucleosome positioning.

  • Segal E
  • Nature
  • 2006 17

Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approximately 50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.