New computational approaches for analysis of cis-regulatory networks.
The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.
Brown
C Titus
CT
Division of Biology 156-29, California Institute of Technology, Pasadena 91125, USA.
Rust
Alistair G
AG
Clarke
Peter J C
PJ
Pan
Zhengjun
Z
Schilstra
Maria J
MJ
De Buysscher
Tristan
T
Griffin
Gareth
G
Wold
Barbara J
BJ
Cameron
R Andrew
RA
Davidson
Eric H
EH
Bolouri
Hamid
H
D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D018076:DNA, Complementary; D005809:Genes, Regulator; D009693:Nucleic Acid Hybridization
D018076:DNA, Complementary