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Items: 1 to 20 of 82


cisRED: a database system for genome-scale computational discovery of regulatory elements.

Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73.


ppdb: a plant promoter database.

Yamamoto YY, Obokata J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D977-81. Epub 2007 Oct 18.


ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Blanco E, Farré D, Albà MM, Messeguer X, Guigó R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D63-7.


Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes.

Pérez AG, Angarica VE, Vasconcelos AT, Collado-Vides J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D132-6. Epub 2006 Nov 6.


SALAD database: a motif-based database of protein annotations for plant comparative genomics.

Mihara M, Itoh T, Izawa T.

Nucleic Acids Res. 2010 Jan;38(Database issue):D835-42. doi: 10.1093/nar/gkp831. Epub 2009 Oct 23.


DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.

Sebestyén E, Nagy T, Suhai S, Barta E.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S6. doi: 10.1186/1471-2105-10-S6-S6.


The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

Marinescu VD, Kohane IS, Riva A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D91-7.


GARSA: genomic analysis resources for sequence annotation.

Dávila AM, Lorenzini DM, Mendes PN, Satake TS, Sousa GR, Campos LM, Mazzoni CJ, Wagner G, Pires PF, Grisard EC, Cavalcanti MC, Campos ML.

Bioinformatics. 2005 Dec 1;21(23):4302-3. Epub 2005 Oct 6.


Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Brown CT, Xie Y, Davidson EH, Cameron RA.

BMC Bioinformatics. 2005 Mar 24;6:70.


JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4.


CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

Hallin PF, Ussery DW.

Bioinformatics. 2004 Dec 12;20(18):3682-6. Epub 2004 Jul 15.


SwissRegulon: a database of genome-wide annotations of regulatory sites.

Pachkov M, Erb I, Molina N, van Nimwegen E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. Epub 2006 Nov 27.


3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

Fleming K, Müller A, MacCallum RM, Sternberg MJ.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D245-50.


MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.


The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

Schmid CD, Praz V, Delorenzi M, Périer R, Bucher P.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D82-5.


A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.

Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL.

PLoS Comput Biol. 2007 Jul;3(7):e126.


SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, Wu Y, Wang J, Mita K, Xiang Z, Xia Q.

Nucleic Acids Res. 2010 Jan;38(Database issue):D453-6. doi: 10.1093/nar/gkp801. Epub 2009 Sep 30.


FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.


Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.

Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D.

Bioinformatics. 2005 Nov 15;21(22):4187-9. Epub 2005 Aug 18.


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