These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
4. CREME: Cis-Regulatory Module Explorer for the human genome. Sharan R; Ben-Hur A; Loots GG; Ovcharenko I Nucleic Acids Res; 2004 Jul; 32(Web Server issue):W253-6. PubMed ID: 15215390 [TBL] [Abstract][Full Text] [Related]
5. Stubb: a program for discovery and analysis of cis-regulatory modules. Sinha S; Liang Y; Siggia E Nucleic Acids Res; 2006 Jul; 34(Web Server issue):W555-9. PubMed ID: 16845069 [TBL] [Abstract][Full Text] [Related]
6. 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. PubMed ID: 17130146 [TBL] [Abstract][Full Text] [Related]
7. PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Ferretti V; Poitras C; Bergeron D; Coulombe B; Robert F; Blanchette M Nucleic Acids Res; 2007 Jan; 35(Database issue):D122-6. PubMed ID: 17148480 [TBL] [Abstract][Full Text] [Related]
8. CONREAL web server: identification and visualization of conserved transcription factor binding sites. Berezikov E; Guryev V; Cuppen E Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W447-50. PubMed ID: 15980509 [TBL] [Abstract][Full Text] [Related]
9. rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Loots GG; Ovcharenko I Nucleic Acids Res; 2004 Jul; 32(Web Server issue):W217-21. PubMed ID: 15215384 [TBL] [Abstract][Full Text] [Related]
10. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Turatsinze JV; Thomas-Chollier M; Defrance M; van Helden J Nat Protoc; 2008; 3(10):1578-88. PubMed ID: 18802439 [TBL] [Abstract][Full Text] [Related]
11. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. Siddharthan R; Siggia ED; van Nimwegen E PLoS Comput Biol; 2005 Dec; 1(7):e67. PubMed ID: 16477324 [TBL] [Abstract][Full Text] [Related]
12. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Marinescu VD; Kohane IS; Riva A Nucleic Acids Res; 2005 Jan; 33(Database issue):D91-7. PubMed ID: 15608292 [TBL] [Abstract][Full Text] [Related]
14. FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Corcoran DL; Feingold E; Benos PV Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W442-6. PubMed ID: 15980508 [TBL] [Abstract][Full Text] [Related]
15. ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors. Papatsenko D Bioinformatics; 2007 Apr; 23(8):1032-4. PubMed ID: 17308342 [TBL] [Abstract][Full Text] [Related]
16. PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Lardenois A; Chalmel F; Bianchetti L; Sahel JA; Léveillard T; Poch O Nucleic Acids Res; 2006 Jul; 34(Web Server issue):W578-83. PubMed ID: 16845074 [TBL] [Abstract][Full Text] [Related]
17. 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; 34(Web Server issue):W584-7. PubMed ID: 16845075 [TBL] [Abstract][Full Text] [Related]
18. A suite of web-based programs to search for transcriptional regulatory motifs. Liu Y; Wei L; Batzoglou S; Brutlag DL; Liu JS; Liu XS Nucleic Acids Res; 2004 Jul; 32(Web Server issue):W204-7. PubMed ID: 15215381 [TBL] [Abstract][Full Text] [Related]
19. P-Match: transcription factor binding site search by combining patterns and weight matrices. Chekmenev DS; Haid C; Kel AE Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W432-7. PubMed ID: 15980505 [TBL] [Abstract][Full Text] [Related]