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

Idan Gabdank; Danny Barash; Edward N. Trifonov

doi:10.1093/bioinformatics/btq030

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

Idan Gabdank, Danny Barash, Edward N. Trifonov

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

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: [email protected].

Original language	English
Article number	btq030
Pages (from-to)	845-846
Number of pages	2
Journal	Bioinformatics
Volume	26
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/btq030
State	Published - 26 Jan 2010

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btq030

Cite this

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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: [email protected].",

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note = "Funding Information: Funding: Pratt fellowship; Lynn and William Frankel Center for Computer Sciences at Ben Gurion University.",

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AU - Barash, Danny

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

Abstract

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