title: Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences.
abstract: This paper describes a novel approach to constructing Position-Specific Weight Matrices (PWMs) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database and comparison of the newly generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were tested and their matrices were compared to the original TRANSFAC matrices. One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences.
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA. bibin@bu.edu
authors.forename: Yutao
authors.initials: Y
authors.lastname: Fu
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D016208:Databases, Factual; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA