FineStr: A web server for single-base-resolution nucleosome positioning

Abstract

Summary: The DNA in eukaryotic cells is packed into the chromatin that is composed of nucleosomes. Positioning of the nucleosome core particles on the sequence is a problem of great interest because of the role nucleosomes play in different cellular processes including gene regulation. Using the sequence structure of 10.4 base DNA repeat presented in our previous works and nucleosome core DNA sequences database, we have derived the complete nucleosome DNA bendability matrix of Caenorhabditis elegans. We have developed a web server named FineStr that allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them. Availability: FineStr server is freely available for use on the web at http:/www.cs.bgu.ac.il/~nucleom. The site contains a help file with explanation regarding the exact usage. Contact: gabdank@cs.bgu.ac.il. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.