MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites

In Silico Biology

Volumn 6, Issue 4, 2006, Pages 307-310

  Su, Gang ^a   Mao, Binchen ^a   Wang, Jin ^a  

^a NANJING UNIVERSITY   (China)

Author keywords

Alignment; Gap; Position Frequency Matrix (PFM); Transcription factor binding site (TFBS)

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BINDING SITE; CLUSTER ANALYSIS; CORRELATION COEFFICIENT; INTERNET; PREDICTION; PROTEIN BINDING; PROTEIN DATABASE; SCORING SYSTEM;

ALGORITHMS; BASE SEQUENCE; BINDING SITES; DNA; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 33748931997     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (9)

1. Matys, V., et al. (2003). TRANSFAC: Transcriptional regulation, from patterns to protiles. Nucleic Acids Res. 31, 1, 374-378.
2. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W. W. and Lenhard, B. (2004). JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94.
3. Schones, D. E., Sumazin, P. and Zhang, M. Q. (2005). Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21, 307-313.
4. Kielbasa, S. M., Gonze, D. and Herzel, H. (2005). Measuring similarities between transcription factor binding sites. BMC Bioinformatics 6, 237.
5. Roepcke, S., Grossmann, S., Rahmann, S. and Vingron, M. (2005). T-Reg Comparator: An analysis tool for the comparison of position weight matrices. Nucleic Acids Res. 33, W438-W441.
6. Hannenhalli, S. and Levy, S. (2002). Predicting transcription factor synergism. Nucleic Acids Res. 30, 4278-4284.
7. Sandelin, A. and Wasserman, W. W. (2004). Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338, 207-215.
8. Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M. and Werner, T. (2005). MatInspector and beyond: Promoter analysis based on transcription factor binding sites. Bioinformatics 21, 2933-2942.
9. Cavener, D. R. (1987). Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res. 15, 1353-1361.