Promoter Analysis Tools

An�lisis y predicci�n de secuencias de promotores bacterianos dependiendo de los factores sigma y alpha y de otros factores reguladores diferentes a la RNAP. Tesis

PAtools web software

Huerta A.M., and Collado-Vides J. "Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals." J Mol Biol. 2003 Oct 17;333(2):261-278.

Create consensi matrices

Hertz, G.Z. and Stormo, G.D. 1999. "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences". Bioinformatics. 15: 563-577.

E.coli K12

The complete genome of Escherichia Coli is presented in the paper: Blattner F.R.; Plunkett III G.; Bloch C.A.; Perna N.T.; Burland V.; Riley M.; Collado-Vides J.; Glasner J.D.; Rode C.K.; Mayhew G.; Gregor J.; Davis N.W.; Kirkpatrick H. A.; Goeden M.A.; Rose D.J.; Mau B.; Shao Y. (1997) "The complete genome sequence of Escherichia coli K-12" Science 277: 1453-1462

Data Base

The information on the database used for promoter predictions is contained in RegulonDB, -see

http://www.cifn.unam.mx/Computational_Genomics/regulondb/

and the associated publications:

Huerta A.M.; Salgado H.; Thieffry D. y Collado-Vides J. (1998) "RegulonDB: A Database on Transcription Regulation in Escherichia coli" Nucleic Acids Res. 26: 55-60

Salgado H.; Santos A.; Garza-Ramos U.; van Helden J.; Díaz E.; and Collado-Vides J. (1999). "RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli" Nucleic Acids Research. 27(1): 59-60.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Millán-Zárate D., Blattner F.R., and Collado-Vides J. (2000) "RegulonDB (version 3.0): Transcriptional Regulation and Operon Organization in Escherichia coli"  Nucleic Acids Research  28: 65-67.

Salgado H. , Santos-Zavaleta A., Gama-Castro S., Millán-Zárate D., Díaz-Peredo E., Sánchez- Solano F., Pérez-Rueda E., Bonavides-Martínez C., and Collado-Vides J. (2001)  "RegulonDB (version 3.2): Transcriptional Regulation and Operon Organization in Escherichia coli K-12", Nucleic Acids Research 29: 72-74.