Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/PercusDecomposition.xml @ 12:81d5b81fb3c2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents b1952a90d4bf
children 3e477c7e0e73
comparison
equal deleted inserted replaced
11:b1952a90d4bf 12:81d5b81fb3c2
8 <outputs> 8 <outputs>
9 <data name="output" format="wig" /> 9 <data name="output" format="wig" />
10 </outputs> 10 </outputs>
11 11
12 <help> 12 <help>
13 .. class:: warningmark 13
14 This tool derives an external potential energy function from experimental nucleosome positioning data by assuming that nucleosomes interact with DNA like a fluid of hard rods. This energy function can then be used to derive sequence-specific nucleosome formation preferences, while accounting for hard-core steric restriction by adjacent nucleosomes. This tool is a reimplementation of the algorithm described in (Locke et al. 2010).
15
16 -----
14 17
15 See Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003 and Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511 for derivation. 18 **Citations**
19
20 Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003
21
22 Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511
23
16 </help> 24 </help>
17 </tool> 25 </tool>