Optimized mixed Markov models for motif identification

[1] Burge C(1997)Prediction of complete gene structures in human genomic DNA J Mol Biol 268 78-94

[2] Karlin S(2003)The Evolution of Transcriptional Regulation in Eukaryotes Mol Biol Evol 20 1377-1419

[3] Wray GA(2003)Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 241-254

[4] Hahn MW(2005)Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex Genome Res 15 692-700

[5] Abouheif E(2005)Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals Nature 434 338-345

[6] Balhoff JP(1984)Computer methods to locate signals in nucleic acid sequences Nucl Acids Res 12 505-519

[7] Pizer M(1998)Specificity, free energy and information content in protein-DNA interactions Trends Biochem Sci 23 109-113

[8] Rockman MV(1995)Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data Nucl Acids Res 23 4878-4884

[9] Romano LA(2003)MATCH: A tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res 31 3576-3579

[10] Kellis M(2001)Non-independence of Mnt represser-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay Nucl Acids Res 29 2471-2478

[1] Burge C(1997)Prediction of complete gene structures in human genomic DNA J Mol Biol 268 78-94

[2] Karlin S(2003)The Evolution of Transcriptional Regulation in Eukaryotes Mol Biol Evol 20 1377-1419

[3] Wray GA(2003)Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 241-254

[4] Hahn MW(2005)Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex Genome Res 15 692-700

[5] Abouheif E(2005)Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals Nature 434 338-345

[6] Balhoff JP(1984)Computer methods to locate signals in nucleic acid sequences Nucl Acids Res 12 505-519

[7] Pizer M(1998)Specificity, free energy and information content in protein-DNA interactions Trends Biochem Sci 23 109-113

[8] Rockman MV(1995)Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data Nucl Acids Res 23 4878-4884

[9] Romano LA(2003)MATCH: A tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res 31 3576-3579

[10] Kellis M(2001)Non-independence of Mnt represser-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay Nucl Acids Res 29 2471-2478