New Computational Approaches for Analysis of cis-Regulatory Networks

Developmental Biology

Zhengjun Pan¹  Tristan De Buysscher¹  Eric H. Davidson¹  Barbara J. Wold¹  R.Andrew Cameron¹  C.Titus Brown¹  Peter J.C. Clarke¹  Maria J. Schilstra¹  Gareth Griffin¹  Alistair G. Rust¹  Hamid Bolouri¹ 

[1] Division of Biology 156-29, California Institute of Technology, Pasadena, California, 91125

关键词: sequence annotation;    comparative analysis;    macroarrays;    gene network modeling;    computational tools;   

DOI  :  10.1006/dbio.2002.0619

学科分类：生物科学（综合）

来源: Academic Press

【 摘 要 】

Theinvestigationandmodelingofgeneregulatorynetworksrequirescomputationaltoolsspecifictothetask.Wepresentseverallocallydevelopedsoftwaretoolsthathavebeenusedinsupportofourongoingresearchintotheembryogenesisoftheseaurchin.Thesetoolsareespeciallywellsuitedtoiterativerefinementofmodelsthroughexperimentalandcomputationalinvestigation.Theyinclude:BioArray,amacroarrayspotprocessingprogram;SUGAR,asystemtodisplayandcorrelatelarge-BACsequenceanalyses;SeqCompandFamilyRelations,programsforcomparativesequenceanalysis;andNetBuilder,anenvironmentforcreatingandanalyzingmodelsofgenenetworks.WealsopresentanoverviewoftheprocessusedtobuildourmodeloftheStrongylocentrotuspurpuratusendomesodermgenenetwork.Severalofthetoolsdiscussedinthispaperarestillinactivedevelopmentandsomeareavailableasopensource.

【 授权许可】

Unknown