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

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Schmid, Christoph D ^a   Praz, Viviane ^a,b   Delorenzi, Mauro ^a,b,c   Périer, Rouaïda ^a   Bucher, Philipp ^a,b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

^c National Center of Competence in Research in Molecular Oncology   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA POLYMERASE II;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; EUKARYOTE; EUKARYOTIC PROMOTER DATABASE; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENETIC TRANSCRIPTION; INTERNET; MOLECULAR CLONING; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA PRIMERS; DNA, COMPLEMENTARY; EUKARYOTIC CELLS; EXPRESSED SEQUENCE TAGS; HUMANS; INTERNET; PROMOTER REGIONS (GENETICS); RESPONSE ELEMENTS; USER-COMPUTER INTERFACE;

EUKARYOTA;

EID: 0348062819     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (20)

1. Bucher,P. and Trifonov,E.N. (1986) Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res., 22, 10009-10026.
2. Bucher,P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
3. Fickett,J.W. and Hatzigeorgiou,A.G. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
4. Baker,W., van den Broek,A., Camon,E., Hingamp,P., Sterk,P., Stoesser,G. and Tuli,M.A. (2000) The EMBL nucleotide sequence database. Nucleic Acids Res., 28, 19-23.
5. Cavin Périer,R., Junier,T. and Bucher,P. (1998) The Eukaryotic Promoter Database EPD. Nucleic Acids Res., 26, 353-357.
6. Cavin Périer,R., Junier,T., Bonnard,C. and Bucher,P. (1999) The Eukaryotic Promoter Database (EPD): recent developments. Nucleic Acids Res., 27, 307-309.
7. Cavin Périer,R., Praz,V., Junier,T., Bonnard,C. and Bucher,P. (2000) The eukaryotic promoter database (EPD). Nucleic Acids Res., 28, 302-303.
8. Praz,V., Jagannathan,V. and Bucher,P. (2004) CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res., 32, D542-D547.
9. Suzuki,Y., Yamashita,R., Nakai,K. and Sugano,S. (2002) DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res., 30, 328-331
10. Sperisen,P., Iseli,C., Pagni,M., Stevenson,B.J., Bucher,P. and Jongeneel,C.V. (2004) trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res., 32, D509-D511.
11. Maire,P., Gautron,S., Hakim,V., Gregori,C., Mennecier,F. and Kahn,A. (1987) Characterization of three optional promoters in the 5′ region of the human aldolase A gene. J. Mol. Biol., 197, 425-438.
12. Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F. et al. Mammalian Gene Collection Program Team (2002) Generation and initial analysis of more than 15 000 full-length human and mouse cDNA sequences. Proc. Natl Acad. Sci. USA, 99, 16899-16903.
13. Stapleton,M., Liao,G.C., Brokstein,P., Hong,L., Carninci,P., Shiraki,T., Hayashizaki,Y., Champe,M., Pacleb,J., Wan,K. et al. (2002) The Drosophila gene collection: Identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res., 12, 1294-1300.
14. Ambrosini,G., Praz,V., Jagannathan,V. and Bucher,P. (2003) Signal search analysis server. Nucleic Acids Res., 31, 3618-3620.
15. Wain,H.M., Lush,M., Ducluzeau,F. and Povey,S. (2002). Genew: the human gene nomenclature database. Nucleic Acids Res., 30, 169-171.
16. Pruitt,K., Tatusov,T. and Manglott,D. (2003) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 31, 34-37.
17. Benson,D.A., Boguski,M., Lipman,D.J. and Ostell,J. (1994) GenBank. Nucleic Acids Res., 22, 3441-3444.
18. Etzold,T., Ulyanov,A. and Argos,P. (1996) SRS: information retrieval system for molecular biology data banks. Methods Enzymol., 266, 114-128.
19. Junier,T. and Bucher,P. (1998) SEView: a Java applet for browsing molecular sequence data. In Silico Biol., 1, 13-20.
20. Falquet,L., Bordoli,L., Ioannidis,V., Pagni,M. and Jongeneel,C.V. (2003) Swiss EMBnet node web server. Nucleic Acids Res., 31, 3782-3783.