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Results: 1 to 20 of 148

1.

PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes.

Yellaboina S, Seshadri J, Kumar MS, Ranjan A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W318-20.

PMID:
15215402
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.

Ranjan S, Seshadri J, Vindal V, Yellaboina S, Ranjan A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W584-7.

PMID:
16845075
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

PMID:
18366802
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

[Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments].

Gerasimova AV, Rodionov DA, Mironov AA, Gel'fand MS.

Mol Biol (Mosk). 2001 Nov-Dec;35(6):1001-9. Russian.

PMID:
11771123
[PubMed - indexed for MEDLINE]
5.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8. doi: 10.1093/nar/gkp894. Epub 2009 Nov 1.

PMID:
19884135
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

CREME: Cis-Regulatory Module Explorer for the human genome.

Sharan R, Ben-Hur A, Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W253-6.

PMID:
15215390
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Regulatory sequence analysis tools.

van Helden J.

Nucleic Acids Res. 2003 Jul 1;31(13):3593-6.

PMID:
12824373
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

ConSite: web-based prediction of regulatory elements using cross-species comparison.

Sandelin A, Wasserman WW, Lenhard B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.

PMID:
15215389
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.

Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11.

PMID:
20542910
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae.

Yellaboina S, Ranjan S, Chakhaiyar P, Hasnain SE, Ranjan A.

BMC Microbiol. 2004 Sep 24;4:38.

PMID:
15447793
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
17130146
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.

González AD, Espinosa V, Vasconcelos AT, Pérez-Rueda E, Collado-Vides J.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D98-102.

PMID:
15608293
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation.

Sinha S, Tompa M.

Nucleic Acids Res. 2003 Jul 1;31(13):3586-8.

PMID:
12824371
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

GRASP-DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs.

Schilling CH, Held L, Torre M, Saier MH Jr.

J Mol Microbiol Biotechnol. 2000 Oct;2(4):495-500.

PMID:
11075923
[PubMed - indexed for MEDLINE]
15.

PRODORIC: prokaryotic database of gene regulation.

Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D.

Nucleic Acids Res. 2003 Jan 1;31(1):266-9.

PMID:
12519998
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability.

Huang Y, Kowalski D.

BMC Bioinformatics. 2004 Sep 21;5:134.

PMID:
15383143
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.

Luo Y, Fu C, Zhang DY, Lin K.

BMC Bioinformatics. 2007 Jul 25;8:266.

PMID:
17650344
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.

Yan B, Lovley DR, Krushkal J.

Biosystems. 2007 Sep-Oct;90(2):421-41. Epub 2006 Oct 26.

PMID:
17184904
[PubMed - indexed for MEDLINE]
19.

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

PMID:
15215395
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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]
Free PMC Article

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