PubMed

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.

Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW.

Nucleic Acids Res. 2009 Jan;37(Database issue):D54-60. Epub 2008 Oct 29.PMID: 18971253 [PubMed - indexed for MEDLINE]Related articlesFree article

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.

Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW.

Genome Biol. 2007;8(10):R207.PMID: 17916232 [PubMed - indexed for MEDLINE]Related articlesFree article

Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements.

Doh ST, Zhang Y, Temple MH, Cai L.

BMC Bioinformatics. 2007 Mar 15;8:94.PMID: 17362514 [PubMed - indexed for MEDLINE]Related articlesFree article

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.

Sierro N, Makita Y, de Hoon M, Nakai K.

Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6. Epub 2007 Oct 25.PMID: 17962296 [PubMed - indexed for MEDLINE]Related articlesFree article

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.

Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D368-72.PMID: 14681436 [PubMed - indexed for MEDLINE]Related articlesFree article

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7.PMID: 18321385 [PubMed - indexed for MEDLINE]Related articlesFree article

In silico detection of sequence variations modifying transcriptional regulation.

Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J.

PLoS Comput Biol. 2008 Jan;4(1):e5. Epub 2007 Nov 27.PMID: 18208319 [PubMed - indexed for MEDLINE]Related articlesFree article

Database of repetitive elements in complete genomes and data mining using transcription factor binding sites.

Horng JT, Lin FM, Lin JH, Huang HD, Liu BJ.

IEEE Trans Inf Technol Biomed. 2003 Jun;7(2):93-100.PMID: 12834164 [PubMed - indexed for MEDLINE]Related articles

ORegAnno: an open-access community-driven resource for regulatory annotation.

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.PMID: 18006570 [PubMed - indexed for MEDLINE]Related articlesFree article

TFBScluster web server for the identification of mammalian composite regulatory elements.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W524-8.PMID: 16845063 [PubMed - indexed for MEDLINE]Related articlesFree article

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

Zhao F, Xuan Z, Liu L, Zhang MQ.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D103-7.PMID: 15608156 [PubMed - indexed for MEDLINE]Related articlesFree article

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.

Marinescu VD, Kohane IS, Riva A.

BMC Bioinformatics. 2005 Mar 30;6:79.PMID: 15799782 [PubMed - indexed for MEDLINE]Related articlesFree article

ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.

BMC Microbiol. 2006 Mar 15;6:29.PMID: 16539733 [PubMed - indexed for MEDLINE]Related articlesFree article

CAGER: classification analysis of gene expression regulation using multiple information sources.

Ruan J, Zhang W.

BMC Bioinformatics. 2005 May 12;6:114.PMID: 15890068 [PubMed - indexed for MEDLINE]Related articlesFree article

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.PMID: 15980535 [PubMed - indexed for MEDLINE]Related articlesFree article

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.

Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70.PMID: 16845071 [PubMed - indexed for MEDLINE]Related articlesFree article

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.PMID: 15655071 [PubMed - indexed for MEDLINE]Related articlesFree article

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.

Edwards YJ, Carver TJ, Vavouri T, Frith M, Bishop MJ, Elgar G.

Nucleic Acids Res. 2003 Jul 1;31(13):3510-7.PMID: 12824356 [PubMed - indexed for MEDLINE]Related articlesFree article

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.PMID: 17445272 [PubMed - indexed for MEDLINE]Related articlesFree article

GeneTools--application for functional annotation and statistical hypothesis testing.

Beisvag V, Jünge FK, Bergum H, Jølsum L, Lydersen S, Günther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A.

BMC Bioinformatics. 2006 Oct 24;7:470.PMID: 17062145 [PubMed - indexed for MEDLINE]Related articlesFree article