Software for the analysis of DNA sequence elements of transcription
GSF-National Research Center for Environment and Health, Institute of Mammalian Genetics, Ingolstudter Landstraße 1, D-85764 Neuherberg Germany
1To whom correspondence should be addressed E-mail: werner{at}gsf.de
The detection of transcription control elements in DNA sequences became both more important and more complicated by the completion of the first full genome sequencing projects. Rapid evaluation of potential regulatory elements in large amounts of sequence data requires specific methods preferably available as user-friendly computer programs. However, many more algorithms and methods have been published than programs are available, creating problems for scientists who try to select an appropriate method for their needs from the literature. The Internet provides a worldwide and relatively easy access to computer software if the user knows where to look. One of the major problems remaining is how to find the appropriate software. We have compiled a guide detailing where software is available and what is to be expected in terms of interface and data compatibility with other programs. We also show results obtained with each program for several examples. The summarized features of each program should allow scientists to select quickly the method of their choice and inform them where to download the software.
Received on September 9, 1996; accepted on September 28, 1996
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. O. Sperber, T. Airola, P. Jern, and J. Blomberg Automated recognition of retroviral sequences in genomic data RetroTector(C) Nucleic Acids Res., August 1, 2007; 35(15): 4964 - 4976. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. V. Sun, D. R. Boverhof, L. D. Burgoon, M. R. Fielden, and T. R. Zacharewski Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences Nucleic Acids Res., August 24, 2004; 32(15): 4512 - 4523. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Pavesi, P. Mereghetti, G. Mauri, and G. Pesole Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes Nucleic Acids Res., July 1, 2004; 32(suppl_2): W199 - W203. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. WERNER, S. FESSELE, H. MAIER, and P. J. NELSON Computer modeling of promoter organization as a tool to study transcriptional coregulation FASEB J, July 1, 2003; 17(10): 1228 - 1237. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. M. Jakt, L. Cao, K. S.E. Cheah, and D. K. Smith Assessing Clusters and Motifs from Gene Expression Data Genome Res., January 1, 2001; 11(1): 112 - 123. [Abstract] [Full Text]
|
|
|
|
|
|
M. S. Gelfand, E. V. Koonin, and A. A. Mironov Prediction of transcription regulatory sites in Archaea by a comparative genomic approach Nucleic Acids Res., February 1, 2000; 28(3): 695 - 705. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Brazma, I. Jonassen, J. Vilo, and E. Ukkonen Predicting Gene Regulatory Elements in Silico on a Genomic Scale Genome Res., November 1, 1998; 8(11): 1202 - 1215. [Abstract] [Full Text]
|
|
|
|
|
|
J. W. Fickett and A. G. Hatzigeorgiou Eukaryotic Promoter Recognition Genome Res., September 1, 1997; 7(9): 861 - 878. [Full Text] [PDF]
|
|