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Tools
Data in AthaMap is based on published transcription factor binding specificities available as alignment matrices or experimentally determined single binding sites. Matrix- and pattern-based screenings were performed to identify potential transcription factor binding sites in the genome of Arabidopsis thaliana (TAIR release 8). The complete list of all transcription factors included in AthaMap, the corresponding references, and screening results are displayed on the documentation page. The description pages explain all tools. By using the search function, the sequence of a specific genomic position or gene can be displayed in a sequence window including the potential transcription factor binding sites. A colocalization function allows the search for user-defined potential combinatorial elements. A set of pre-calculated known combinatorial elements is already incorporated in AthaMap. The Gene Analysis tool enables identification of common transcription factor binding sites in a set of user-submitted genes. The Gene Identification tool allows the search for transcription factor binding sites of a specific transcription factor. The Small RNA Targets tool enables identification of small RNA target genes. The MicroRNA Targets tool identifies target genes of miRNAs.

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