SIGNAL SCAN 4.0: additional databases and sequence formats

SIGNAL SCAN is a program that utilizes transcription factor databases to find potential transcription factor binding sites in DNA sequences. The program is now in its fourth version. SIGNAL SCAN 4 now includes, in addition to the Transcription Factor Database, the TRANSFAC and IMD (Information Matrix Database) databases. In addition, it now accepts GCG and FASTA formatted DNA sequences in addition to Staden formatted sequences. SIGNAL SCAN is available for both IBM-compatible PC and Unix workstation platforms.

[1]  E. Wingender,et al.  Recognition of regulatory regions in genomic sequences. , 1994, Journal of biotechnology.

[2]  C S Song,et al.  A distal activation domain is critical in the regulation of the rat androgen receptor gene promoter. , 1993, The Biochemical journal.

[3]  G. Stormo.  Computer methods for analyzing sequence recognition of nucleic acids. , 1988, Annual Review of Biophysics and Biophysical Chemistry.

[4]  C Burks,et al.  The density of transcriptional elements in promoter and non-promoter sequences. , 1993, Human molecular genetics.

[5]  B. Brunk,et al.  Embryonic activation of the myoD gene is regulated by a highly conserved distal control element. , 1995, Development.

[6]  R. KNÜPPEL,et al.  TRANSFAC Retrieval Program: A Network Model Database of Eukaryotic Transcription Regulating Sequences and Proteins , 1994, J. Comput. Biol..

[7]  Gary D. Stormo,et al.  MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices , 1995, Comput. Appl. Biosci..

[8]  G. Pari,et al.  Boundaries and structure of human cytomegalovirus oriLyt, a complex origin for lytic-phase DNA replication , 1992, Journal of virology.

[9]  J. Fickett.  Quantitative discrimination of MEF2 sites , 1996, Molecular and cellular biology.

[10]  E. Wingender,et al.  Transcription regulating proteins and their recognition sequences. , 1990, Critical reviews in eukaryotic gene expression.

[11]  J. Fickett.  Copyright � 1996, American Society for Microbiology Quantitative Discrimination of MEF2 Sites , 1995 .

[12]  J. Benovic,et al.  Structure of the human gene encoding the beta-adrenergic receptor kinase. , 1994, The Journal of biological chemistry.

[13]  I. Verma,et al.  Autoregulation of I kappa B alpha activity. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[14]  D. S. Prestridge.  Predicting Pol II promoter sequences using transcription factor binding sites. , 1995, Journal of molecular biology.

[15]  W. Pearson.  Rapid and sensitive sequence comparison with FASTP and FASTA. , 1990, Methods in enzymology.

[16]  W. G. Hoeck,et al.  InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface , 1994, Comput. Appl. Biosci..

[17]  D. Ghosh,et al.  New developments of a transcription factors database. , 1991, Trends in biochemical sciences.

[18]  Gary D. Stormo,et al.  SIGNAL SCAN 3.0: new database and program features , 1993, Comput. Appl. Biosci..

[19]  Dan S. Prestridge,et al.  SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements , 1991, Comput. Appl. Biosci..