title: TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
abstract: TAMO (Tools for Analysis of MOtifs) is an object-oriented computational framework for interpreting transcriptional regulation using DNA-sequence motifs. To simplify the application of multiple motif discovery programs to genome-wide data, TAMO provides a sophisticated motif object with interfaces to several popular programs. In addition, TAMO provides modules for integrating motif analysis with diverse data sources including genomic sequences, microarrays and various databases. Finally, TAMO includes tools for sequence analysis, algorithms for scoring, comparing and clustering motifs, and several useful statistical tests. Recently, we have applied these tools to analyze tens of thousands of motifs derived from hundreds of microarray experiments.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center Cambridge, MA 02142, USA.
authors.forename: D Benjamin
authors.initials: DB
authors.lastname: Gordon
authors.forename: Lena
authors.initials: L
authors.lastname: Nekludova
authors.forename: Scott
authors.initials: S
authors.lastname: McCallum
authors.forename: Ernest
authors.initials: E
authors.lastname: Fraenkel
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014158:Transcription, Genetic / Q000235:genetics*